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resal81/NAMD CVS with `colvars on`

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NAMD CVS high `dE_avg` values
Raw
README.md

When compiling NAMD CVS and colvars git on Stampede, the dE_avg energies are very high and incorrect.

Loaded modules

$ module list
  1) intel/15.0.2   2) mvapich2/2.1   3) xalt/0.6   4) TACC

Compile script

#!/usr/bin/env bash

set -e

NAMD_VERSION="2016-05-09"

download_namd () {
    wget http://www.ks.uiuc.edu/Research/namd/cvs/download/741376/NAMD_CVS-${NAMD_VERSION}_Source.tar.gz
    tar xzf NAMD_CVS-${NAMD_VERSION}_Source.tar.gz
    ln -s NAMD_CVS-${NAMD_VERSION}_Source namd_cvs
}

download_colvars () {
    wget https://github.com/colvars/colvars/archive/master.zip
    unzip master.zip
    ln -s colvars-master colvars
}

download_fftw_tcl () {
    cd namd_cvs

    wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
    tar xzf fftw-linux-x86_64.tar.gz
    ln -s linux-x86_64 fftw

    wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
    tar xzf tcl8.5.9-linux-x86_64.tar.gz
    ln -s tcl8.5.9-linux-x86_64 tcl

    wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
    tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
    ln -s tcl8.5.9-linux-x86_64-threaded tcl-threaded

    cd ..
}

patch_namd () {
    cd colvars
    ./update-colvars-code.sh -f ../namd_cvs
    cd ..
}

compile_charm () {
    cd namd_cvs

    tar xf charm-*
    cd charm-*
    env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --no-build-shared --with-production

    cd ../..
}

config_namd () {
    cd namd_cvs
    ./config Linux-x86_64-icc --charm-arch mpi-linux-x86_64
    cd ..
}

compile_namd () {
    cd namd_cvs
    cd Linux-x86_64-icc 

    make depends
    make -j 4 release
    
    cd ../..
}

download_namd 
download_colvars
download_fftw_tcl

patch_namd

compile_charm

config_namd
compile_namd
Raw
NAMD CVS with `colvars on`
```
# STEP Elec vdW dE dE_avg Temp dG
# l l+dl l l+dl E(l+dl)-E(l)
#NEW FEP WINDOW: LAMBDA SET TO 0 LAMBDA2 0.05
FepEnergy: 50 -173267.1741 -173265.5731 3721.3632 3721.3632 1.6010 -36368.9256 299.8270 -9999999999.9999
FepEnergy: 100 -172961.1502 -172958.8260 3480.1072 3480.1072 2.3242 -36363.8878 299.2973 -9999999999.9999
FepEnergy: 150 -173046.4077 -173044.0104 3545.0965 3545.0965 2.3973 -36364.7943 298.6183 -9999999999.9999
FepEnergy: 200 -173126.0777 -173123.8534 3507.0219 3507.0219 2.2243 -36357.7866 300.8991 -9999999999.9999
FepEnergy: 250 -173144.6532 -173142.3190 3543.7177 3543.7177 2.3342 -36349.6853 299.4086 -9999999999.9999
```
```
TACC: Starting up job 7023336
TACC: Setting up parallel environment for MVAPICH2+mpispawn.
TACC: Starting parallel tasks...
Charm++> Running on MPI version: 3.0
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE)
Charm++> Running in non-SMP mode: numPes 256
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.7.1-rc1-0-gbdf6a1b-namd-charm-6.7.1-build-2016-Apr-16-49226
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 16 unique compute nodes (16-way SMP).
Charm++> cpu topology info is gathered in 0.032 seconds.
Info: NAMD 2.11 for Linux-x86_64-MPI
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60701 for mpi-linux-x86_64
Info: Built Mon May 9 10:46:23 CDT 2016 by tg804216 on login2.stampede.tacc.utexas.edu
Info: 1 NAMD 2.11 Linux-x86_64-MPI 256 c470-904.stampede.tacc.utexas.edu tg804216
Info: Running on 256 processors, 256 nodes, 16 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.122841 s
Info: 273.676 MB of memory in use based on /proc/self/stat
Info: Configuration file is FEP01.conf
Info: Working in the current directory /scratch/01143/tg804216/proj8/SimsInputs/3D4S/fepK6
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE eq9.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 81.2352 0 0
Info: PERIODIC CELL BASIS 2 0 80.2855 0
Info: PERIODIC CELL BASIS 3 0 0 101.861
Info: PERIODIC CELL CENTER 0 0 0
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: REMOVING LOAD FROM NODE 0
Info: REMOVING PATCHES FROM PROCESSOR 0
Info: MIN ATOMS PER PATCH 40
Info: VELOCITY FILE eq9.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME fep01.dcd
Info: DCD FREQUENCY 2500
Info: DCD FIRST STEP 2500
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME fep01.xst
Info: XST FREQUENCY 2500
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME fep01
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME fep01.restart
Info: RESTART FREQUENCY 2500
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: VDW FORCE SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 14
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 1.008
Info: HYDROGEN GROUP CUTOFF 2.8
Info: PATCH DIMENSION 17.808
Info: ENERGY OUTPUT STEPS 2500
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 2500
Info: ALCHEMICAL FEP ON
Info: FEP CURRENT LAMBDA VALUE 0
Info: FEP COMPARISON LAMBDA VALUE 0.05
Info: FEP INTRA-ALCHEMICAL NON-BONDED INTERACTIONS WILL BE RETAINED
Info: FEP INTRA-ALCHEMICAL BONDED INTERACTIONS WILL BE RETAINED
Info: FEP VDW SHIFTING COEFFICIENT 6
Info: FEP ELEC. ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 0.5
Info: FEP ELEC. ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0.5 AND LAMBDA = 1
Info: FEP VDW ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0.5 AND LAMBDA = 1
Info: FEP VDW ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 0.5
Info: FEP BOND ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 1
Info: FEP BOND ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 1
Info: COLLECTIVE VARIABLES CALCULATION REQUESTED
Info: COLLECTIVE VARIABLES CONFIGURATION rest.in
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 0.1 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1 BAR
Info: OSCILLATION PERIOD IS 200 FS
Info: DECAY TIME IS 100 FS
Info: PISTON TEMPERATURE IS 300 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 2.03684e-05 2.03684e-05 -4.36381e-07
Info: CELL FLUCTUATION IS ANISOTROPIC
Info: SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 6
Info: PME GRID DIMENSIONS 84 84 108
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from FFTW_NAMD_2.11_Linux-x86_64-MPI.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.11_Linux-x86_64-MPI.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1462873598
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ../out7_ions.pdb
Info: STRUCTURE FILE ../out7_ions.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ../../toppar/par_all36_prot.prm
Info: PARAMETERS ../../toppar/par_all36_na.prm
Info: PARAMETERS ../../toppar/par_all36_carb.prm
Info: PARAMETERS ../../toppar/par_all36_lipid.prm
Info: PARAMETERS ../../toppar/par_all36_cgenff.prm
Info: PARAMETERS ../../toppar/chol.prm
Info: PARAMETERS ../../toppar/wation.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES eq9.coor
Warning: SKIPPING PART OF PARAMETER FILE AFTER RETURN STATEMENT
Info: SUMMARY OF PARAMETERS:
Info: 939 BONDS
Info: 2773 ANGLES
Info: 6799 DIHEDRAL
Info: 193 IMPROPER
Info: 6 CROSSTERM
Info: 350 VDW
Info: 23 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: Residue 20 out of order in segment O1, lookup for additional residues in this segment disabled.
Info: TIME FOR READING PSF FILE: 7.88427
Info: Reading pdb file ../out7_ions.pdb
Info: TIME FOR READING PDB FILE: 0.124348
Info:
Info: To read alchdata from file: ../out9_alchfile.pdb
Info: To read alchflag data from column: 5
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 69634 ATOMS
Info: 56966 BONDS
Info: 73525 ANGLES
Info: 88042 DIHEDRALS
Info: 1032 IMPROPERS
Info: 275 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 56919 RIGID BONDS
Info: ALCH: 74 ATOMS TO DISAPPEAR IN FINAL STATE
Info: ALCH: 0 ATOMS TO APPEAR IN FINAL STATE
Info: 151983 DEGREES OF FREEDOM
Info: 25417 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 25417 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 413314 amu
Info: TOTAL CHARGE = 9.818e-06 e
Info: MASS DENSITY = 1.03312 g/cm^3
Info: ATOM DENSITY = 0.104817 atoms/A^3
Info: *****************************
Info: Reading from binary file eq9.coor
Info:
Info: Entering startup at 29.7645 s, 399.152 MB of memory in use
Info: Startup phase 0 took 0.00476599 s, 399.152 MB of memory in use
Info: ADDED 217340 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.125727 s, 410.609 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.6778e-33 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 3.71539e-17 AT 11.9974
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 9.34011e-27 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 2.98256e-17 AT 11.9974
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.0123639 s, 414.352 MB of memory in use
Info: Startup phase 3 took 0.000324965 s, 414.352 MB of memory in use
Info: Startup phase 4 took 0.00302601 s, 414.352 MB of memory in use
Info: Startup phase 5 took 0.000293016 s, 414.352 MB of memory in use
Info: PATCH GRID IS 9 (PERIODIC) BY 4 (PERIODIC) BY 5 (PERIODIC)
Info: PATCH GRID IS 2-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file eq9.vel
Info: REMOVING COM VELOCITY 0.00634616 0.00950085 -0.00831659
Info: LARGEST PATCH (136) HAS 435 ATOMS
Info: TORUS A SIZE 256 USING 0 16 32 48 64 80 96 112 128 144 160 176 192 208 224 240
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 241 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.061497 s, 430.035 MB of memory in use
Info: PME using 42 and 42 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 7 15 23 27 31 39 47 55 59 63 ...
Info: PME TRANS LOCATIONS: 3 11 13 19 29 35 43 45 51 53 ...
Info: PME USING 42 GRID NODES AND 42 TRANS NODES
Info: Startup phase 7 took 0.0121171 s, 430.035 MB of memory in use
Info: Startup phase 8 took 0.076756 s, 435.191 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.0531468 s, 435.191 MB of memory in use
Info: CREATING 6300 COMPUTE OBJECTS
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2016-05-03.
colvars: Please cite Fiorin et al, Mol Phys 2013 in any publication based on this calculation.
colvars: Using NAMD interface, version 2016-04-28.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "rest.in":
colvars: # indexFile = "" [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 500
colvars: # colvarsRestartFrequency = 500
colvars: # colvarsTrajAppend = off [default]
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = on [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = rmsd_rest_402
colvars: Initializing a new "rmsd" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # scalable = on [default]
colvars: Scalable calculation is not available for group "atoms" with the current configuration.
colvars: Initializing atom group "atoms".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = on
colvars: # rotateReference = on
colvars: # enableFitGradients = on [default]
colvars: Within atom group "atoms":
colvars: Defining atom group "refPositionsGroup".
colvars: Initializing atom group "refPositionsGroup".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = rest_ref.pdb
colvars: # atomsCol = O
colvars: # atomsColValue = 0 [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "refPositionsGroup" defined, 88 atoms initialized: total mass = 1056.97, total charge = 5.84.
colvars: # refPositions = [default]
colvars: # refPositionsFile = rest_ref.pdb
colvars: # refPositionsCol = "" [default]
colvars: Warning: atom group "atoms" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use refPositionsGroup (or a different definition for it if already defined) to align the coordinates.
colvars: Atom group "atoms" defined, 11 atoms initialized: total mass = 132.121, total charge = -1.23.
colvars: The option "refPositionsGroup" (alternative group for fitting) was enabled: Jacobian derivatives of the RMSD will not be calculated.
colvars: # refPositions = [default]
colvars: # refPositionsFile = rest_ref.pdb
colvars: # refPositionsCol = "" [default]
colvars: WARNING: explicit fitting parameters were provided for atom group "atoms".
colvars: All components initialized.
colvars: # width = 1
colvars: # lowerBoundary = 0
colvars: # lowerWallConstant = 0
colvars: # upperBoundary = 0.7
colvars: # upperWallConstant = 100
colvars: # upperWall = 0.7 [default]
colvars: # hardLowerBoundary = off [default]
colvars: # hardUpperBoundary = off [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = chol_dist
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # scalable = on [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Will enable scalable calculation for group "group1".
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = on
colvars: # rotateReference = on
colvars: # enableFitGradients = on [default]
colvars: Within atom group "group1":
colvars: Defining atom group "refPositionsGroup".
colvars: Initializing atom group "refPositionsGroup".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = rest_ref.pdb
colvars: # atomsCol = O
colvars: # atomsColValue = 0 [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "refPositionsGroup" defined, 88 atoms initialized: total mass = 1056.97, total charge = 5.84.
colvars: # refPositions = [default]
colvars: # refPositionsFile = rest_ref.pdb
colvars: # refPositionsCol = "" [default]
colvars: Warning: atom group "group1" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use refPositionsGroup (or a different definition for it if already defined) to align the coordinates.
colvars: Atom group "group1" defined, 11 atoms initialized: total mass = 132.121, total charge = -1.23.
colvars: Will enable scalable calculation for group "group2".
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0.827 , 0.65 , -2.623 )
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 0 atoms initialized: total mass = 1, total charge = 0.
colvars: All components initialized.
colvars: # width = 1
colvars: # lowerBoundary = 0
colvars: # lowerWallConstant = 0
colvars: # upperBoundary = 3
colvars: # upperWallConstant = 100
colvars: # upperWall = 3 [default]
colvars: # hardLowerBoundary = off [default]
colvars: # hardUpperBoundary = off [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "harmonic1" [default]
colvars: # colvars = { rmsd_rest_402 }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 0
colvars: # centers = { 0 }
colvars: # targetCenters = { 0 } [default]
colvars: # targetForceConstant = 0 [default]
colvars: # outputCenters = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "harmonic2" [default]
colvars: # colvars = { chol_dist }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 0
colvars: # centers = { 0 }
colvars: # targetCenters = { 0 } [default]
colvars: # targetForceConstant = 0 [default]
colvars: # outputCenters = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Updating NAMD interface:
colvars: updating atomic data (99 atoms).
colvars: updating group data (1 scalable groups, 11 atoms in total).
colvars: Re-initialized atom group rmsd_rest_402:0/0. 11 atoms: total mass = 132.121.
colvars: Re-initialized atom group chol_dist:0/0. 11 atoms: total mass = 132.121.
colvars: Re-initialized atom group chol_dist:0/1. 0 atoms: total mass = 1.
colvars: The restart output state file will be "fep01.restart.colvars.state".
colvars: The final output state file will be "fep01.colvars.state".
colvars: Writing to colvar trajectory file "fep01.colvars.traj".
Info: Startup phase 10 took 0.543938 s, 435.191 MB of memory in use
Info: useSync: 1 useProxySync: 0
Info: Startup phase 11 took 0.000968933 s, 435.191 MB of memory in use
Info: Startup phase 12 took 0.000125885 s, 435.191 MB of memory in use
Info: Finished startup at 30.6595 s, 435.191 MB of memory in use
TCL: Running for 1000000 steps
colvars: Updating NAMD interface:
colvars: updating atomic data (99 atoms).
colvars: updating group data (1 scalable groups, 11 atoms in total).
FEP: RESETTING FOR NEW FEP WINDOW LAMBDA SET TO 0 LAMBDA2 0.05
FEP: WINDOW TO HAVE 300000 STEPS OF EQUILIBRATION PRIOR TO FEP DATA COLLECTION.
FEP: USING CONSTANT TEMPERATURE OF 300 K FOR FEP CALCULATION
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 3890.8379 19121.1035 12892.7708 231.7270 -173040.0542 3646.2544 0.0000 0.0000 45249.3689 -88007.9917 299.6456 -133257.3606 -87684.2150 299.6456 94.2039 118.9193 664336.2988 94.2039 118.9193
OPENING FEP ENERGY OUTPUT FILE
OPENING EXTENDED SYSTEM TRAJECTORY FILE
LDB: ============= START OF LOAD BALANCING ============== 31.0167
LDB: ============== END OF LOAD BALANCING =============== 31.039
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 31.0398
LDB: ============= START OF LOAD BALANCING ============== 31.9022
LDB: Largest compute 2586 load 0.120326 is 30.1% of average load 0.399465
LDB: Average compute 0.012671 is 3.2% of average load 0.399465
LDB: Partitioning computes with target load 0.039947
LDB: Increased migratable compute count from 5040 to 5680
LDB: Largest unpartitionable compute is 0.018083
```
Raw
NAMD CVS without `colvars on`
```
# STEP Elec vdW dE dE_avg Temp dG
# l l+dl l l+dl E(l+dl)-E(l)
#NEW FEP WINDOW: LAMBDA SET TO 0 LAMBDA2 0.05
FepEnergy: 50 -173196.7541 -173195.1787 3743.5825 3743.5825 1.5753 -36364.5573 299.2817 -9999999999.9999
FepEnergy: 100 -173253.7368 -173251.5123 3579.6173 3579.6173 2.2245 -36351.0122 300.3906 -9999999999.9999
FepEnergy: 150 -172689.4665 -172687.1104 3386.5257 3386.5257 2.3561 -36356.4400 297.5222 -9999999999.9999
FepEnergy: 200 -172956.2206 -172954.0902 3409.1576 3409.1576 2.1304 -36352.6215 300.2071 -9999999999.9999
FepEnergy: 250 -173035.0248 -173032.8030 3664.4997 3664.4997 2.2218 -36346.8634 297.8605 -9999999999.9999
```
```
TACC: Starting up job 7064583
TACC: Setting up parallel environment for MVAPICH2+mpispawn.
TACC: Starting parallel tasks...
Charm++> Running on MPI version: 3.0
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE)
Charm++> Running in non-SMP mode: numPes 16
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.7.1-rc1-0-gbdf6a1b-namd-charm-6.7.1-build-2016-Apr-16-49226
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (16-way SMP).
Charm++> cpu topology info is gathered in 0.013 seconds.
Info: NAMD 2.11 for Linux-x86_64-MPI
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60701 for mpi-linux-x86_64
Info: Built Mon May 9 10:46:23 CDT 2016 by tg804216 on login2.stampede.tacc.utexas.edu
Info: 1 NAMD 2.11 Linux-x86_64-MPI 16 c560-703.stampede.tacc.utexas.edu tg804216
Info: Running on 16 processors, 16 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.03054 s
Info: 263.52 MB of memory in use based on /proc/self/stat
Info: Configuration file is FEP01.conf
Info: Working in the current directory /scratch/01143/tg804216/proj8/SimsInputs/3D4S/test_namd_mailing_list
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE eq9.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 81.2352 0 0
Info: PERIODIC CELL BASIS 2 0 80.2855 0
Info: PERIODIC CELL BASIS 3 0 0 101.861
Info: PERIODIC CELL CENTER 0 0 0
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: VELOCITY FILE eq9.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME fep01.dcd
Info: DCD FREQUENCY 2500
Info: DCD FIRST STEP 2500
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME fep01.xst
Info: XST FREQUENCY 2500
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME fep01
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME fep01.restart
Info: RESTART FREQUENCY 2500
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: VDW FORCE SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 14
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 1.008
Info: HYDROGEN GROUP CUTOFF 2.8
Info: PATCH DIMENSION 17.808
Info: ENERGY OUTPUT STEPS 2500
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 2500
Info: ALCHEMICAL FEP ON
Info: FEP CURRENT LAMBDA VALUE 0
Info: FEP COMPARISON LAMBDA VALUE 0.05
Info: FEP INTRA-ALCHEMICAL NON-BONDED INTERACTIONS WILL BE RETAINED
Info: FEP INTRA-ALCHEMICAL BONDED INTERACTIONS WILL BE RETAINED
Info: FEP VDW SHIFTING COEFFICIENT 6
Info: FEP ELEC. ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 0.5
Info: FEP ELEC. ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0.5 AND LAMBDA = 1
Info: FEP VDW ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0.5 AND LAMBDA = 1
Info: FEP VDW ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 0.5
Info: FEP BOND ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 1
Info: FEP BOND ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 1
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 0.1 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1 BAR
Info: OSCILLATION PERIOD IS 200 FS
Info: DECAY TIME IS 100 FS
Info: PISTON TEMPERATURE IS 300 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 2.03684e-05 2.03684e-05 -4.36381e-07
Info: CELL FLUCTUATION IS ANISOTROPIC
Info: SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 6
Info: PME GRID DIMENSIONS 84 84 108
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from FFTW_NAMD_2.11_Linux-x86_64-MPI.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.11_Linux-x86_64-MPI.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1463511698
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ../out7_ions.pdb
Info: STRUCTURE FILE ../out7_ions.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ../../toppar/par_all36_prot.prm
Info: PARAMETERS ../../toppar/par_all36_na.prm
Info: PARAMETERS ../../toppar/par_all36_carb.prm
Info: PARAMETERS ../../toppar/par_all36_lipid.prm
Info: PARAMETERS ../../toppar/par_all36_cgenff.prm
Info: PARAMETERS ../../toppar/chol.prm
Info: PARAMETERS ../../toppar/wation.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES eq9.coor
Warning: SKIPPING PART OF PARAMETER FILE AFTER RETURN STATEMENT
Info: SUMMARY OF PARAMETERS:
Info: 939 BONDS
Info: 2773 ANGLES
Info: 6799 DIHEDRAL
Info: 193 IMPROPER
Info: 6 CROSSTERM
Info: 350 VDW
Info: 23 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 7.79616
Info: Reading pdb file ../out7_ions.pdb
Info: TIME FOR READING PDB FILE: 0.133814
Info:
Info: To read alchdata from file: ../out9_alchfile.pdb
Info: To read alchflag data from column: 5
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 69634 ATOMS
Info: 56966 BONDS
Info: 73525 ANGLES
Info: 88042 DIHEDRALS
Info: 1032 IMPROPERS
Info: 275 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 56919 RIGID BONDS
Info: ALCH: 74 ATOMS TO DISAPPEAR IN FINAL STATE
Info: ALCH: 0 ATOMS TO APPEAR IN FINAL STATE
Info: 151983 DEGREES OF FREEDOM
Info: 25417 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 25417 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 413314 amu
Info: TOTAL CHARGE = 9.818e-06 e
Info: MASS DENSITY = 1.03312 g/cm^3
Info: ATOM DENSITY = 0.104817 atoms/A^3
Info: *****************************
Info: Reading from binary file eq9.coor
Info:
Info: Entering startup at 15.4427 s, 388.672 MB of memory in use
Info: Startup phase 0 took 0.000266075 s, 388.672 MB of memory in use
Info: ADDED 217340 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.0929978 s, 399.961 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.6778e-33 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 3.71539e-17 AT 11.9974
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 9.34011e-27 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 2.98256e-17 AT 11.9974
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.00519609 s, 403.703 MB of memory in use
Info: Startup phase 3 took 0.000176907 s, 403.703 MB of memory in use
Info: Startup phase 4 took 0.000459194 s, 403.703 MB of memory in use
Info: Startup phase 5 took 0.000149965 s, 403.703 MB of memory in use
Info: PATCH GRID IS 4 (PERIODIC) BY 4 (PERIODIC) BY 5 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file eq9.vel
Info: REMOVING COM VELOCITY 0.00634616 0.00950085 -0.00831659
Info: LARGEST PATCH (53) HAS 953 ATOMS
Info: TORUS A SIZE 16 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.0989609 s, 419.773 MB of memory in use
Info: PME using 14 and 14 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 9 10 11 ...
Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
Info: PME USING 14 GRID NODES AND 14 TRANS NODES
Info: Startup phase 7 took 0.00398707 s, 419.773 MB of memory in use
Info: Startup phase 8 took 0.00150204 s, 419.773 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.00158787 s, 419.773 MB of memory in use
Info: CREATING 1680 COMPUTE OBJECTS
Info: Startup phase 10 took 0.00396109 s, 419.773 MB of memory in use
Info: useSync: 0 useProxySync: 0
Info: Startup phase 11 took 0.000231028 s, 419.773 MB of memory in use
Info: Startup phase 12 took 0.00045085 s, 419.773 MB of memory in use
Info: Finished startup at 15.6526 s, 419.773 MB of memory in use
TCL: Running for 1000000 steps
FEP: RESETTING FOR NEW FEP WINDOW LAMBDA SET TO 0 LAMBDA2 0.05
FEP: WINDOW TO HAVE 300000 STEPS OF EQUILIBRATION PRIOR TO FEP DATA COLLECTION.
FEP: USING CONSTANT TEMPERATURE OF 300 K FOR FEP CALCULATION
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 3890.8379 19121.1035 12892.7708 231.7270 -173040.0543 3646.2544 0.0000 0.0000 45249.3689 -88007.9917 299.6456 -133257.3606 -87684.2150 299.6456 94.2039 118.9193 664336.2988 94.2039 118.9193
OPENING FEP ENERGY OUTPUT FILE
OPENING EXTENDED SYSTEM TRAJECTORY FILE
LDB: ============= START OF LOAD BALANCING ============== 17.5456
LDB: ============== END OF LOAD BALANCING =============== 17.5468
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 17.5473
LDB: ============= START OF LOAD BALANCING ============== 25.0131
LDB: Largest compute 143 load 0.330664 is 4.7% of average load 7.000561
LDB: Average compute 0.040349 is 0.6% of average load 7.000561
LDB: Partitioning computes with target load 0.700056
LDB: Increased migratable compute count from 1520 to 1520
LDB: Largest unpartitionable compute is 0.039669
```
@resal81
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Author

resal81 commented May 19, 2016

Test using TI (alchType TI) and same seed as simulation above with FEP

ti.out

#TITITLE:    TS          BOND1       AVGBOND1         ELECT1      AVGELECT1                VDW1        AVGVDW1          BOND2       AVGBOND2         ELECT2           AVGELECT2           VDW2        AVGVDW2
#NEW TI WINDOW: LAMBDA 0
#PARTITION 1 BOND LAMBDA 0
#PARTITION 1 VDW LAMBDA 0
#PARTITION 1 ELEC LAMBDA 0
#PARTITION 2 BOND LAMBDA 1
#PARTITION 2 VDW LAMBDA 1
#PARTITION 2 ELEC LAMBDA 1
#CONSTANT TEMPERATURE: 300 K
TI:           0         0.0000         0.0000         0.0000        -0.0406              0.0000        -2.8123         0.0000        -0.0472       -21.5365             -5.3881         1.1366        -1.0988
TI:          10         0.0000         0.0000         0.0000        -0.0116              0.0000        -0.8035         0.0000        -0.0135       -21.0105            -16.5470        -8.0542        -6.0670
TI:          20         0.0000         0.0000         0.0000        -0.0068              0.0000        -0.4687         0.0000        -0.0079       -20.5246            -18.2043         0.2874        -3.4193
TI:          30         0.0000         0.0000         0.0000        -0.0048              0.0000        -0.3309         0.0000        -0.0056       -21.6674            -19.2229         0.6446        -2.2240
TI:          40         0.0000         0.0000         0.0000        -0.0037              0.0000        -0.2557         0.0000        -0.0043       -19.1904            -19.2155        10.2638         0.6141
TI:          50         0.0000         0.0000         0.0000        -0.0030              0.0000        -0.2083         0.0000        -0.0035       -17.1250            -18.8284        22.3775         4.6444
TI:          60         0.0000         0.0000         0.0000        -0.0025              0.0000        -0.1758         0.0000        -0.0030       -18.5001            -18.7771        35.8848         9.5257
TI:          70         0.0000         0.0000         0.0000        -0.0022              0.0000        -0.1520         0.0000        -0.0026       -19.6587            -18.8962        37.4888        13.3045
TI:          80         0.0000         0.0000         0.0000        -0.0019              0.0000        -0.1339         0.0000        -0.0022       -19.1000            -18.9205         8.6598        12.7515
TI:          90         0.0000         0.0000         0.0000        -0.0017              0.0000        -0.1197         0.0000        -0.0020       -21.0103            -19.1428        -0.4558        11.3465
TI:         100         0.0000         0.0000         0.0000        -0.0016              0.0000        -0.1082         0.0000        -0.0018       -21.8487            -19.4030        -5.9104         9.6872
TI:         110         0.0000         0.0000         0.0000        -0.0014              0.0000        -0.0987         0.0000        -0.0017       -23.7153            -19.7813         3.8981         9.1794
TI:         120         0.0000         0.0000         0.0000        -0.0013              0.0000        -0.0907         0.0000        -0.0015       -25.6152            -20.2517        19.0981         9.9793
TI:         130         0.0000         0.0000         0.0000        -0.0012              0.0000        -0.0839         0.0000        -0.0014       -24.5477            -20.5723        44.3298        12.5427
TI:         140         0.0000         0.0000         0.0000        -0.0011              0.0000        -0.0781         0.0000        -0.0013       -23.6354            -20.7850         4.5528        11.9879
TI:         150         0.0000         0.0000         0.0000        -0.0011              0.0000        -0.0730         0.0000        -0.0012       -22.1782            -20.8755         7.9915        11.7284
TI:         160         0.0000         0.0000         0.0000        -0.0010              0.0000        -0.0686         0.0000        -0.0012       -21.5031            -20.9138         4.2547        11.2727
TI:         170         0.0000         0.0000         0.0000        -0.0009              0.0000        -0.0647         0.0000        -0.0011       -20.8738            -20.9115        14.5348        11.4601
TI:         180         0.0000         0.0000         0.0000        -0.0009              0.0000        -0.0611         0.0000        -0.0010       -21.5155            -20.9443        28.4896        12.3856
TI:         190         0.0000         0.0000         0.0000        -0.0008              0.0000        -0.0580         0.0000        -0.0010       -21.0862            -20.9516        27.0760        13.1429
TI:         200         0.0000         0.0000         0.0000        -0.0008              0.0000        -0.0551         0.0000        -0.0009       -18.6317            -20.8379        10.4825        13.0125

logfile

TACC: Starting up job 7075425
TACC: Setting up parallel environment for MVAPICH2+mpispawn.
TACC: Starting parallel tasks...
Charm++> Running on MPI version: 3.0
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE)
Charm++> Running in non-SMP mode: numPes 16
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.7.1-rc1-0-gbdf6a1b-namd-charm-6.7.1-build-2016-Apr-16-49226
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.  
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (16-way SMP).
Charm++> cpu topology info is gathered in 0.014 seconds.
Info: NAMD 2.11 for Linux-x86_64-MPI
Info: 
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info: 
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: 
Info: Based on Charm++/Converse 60701 for mpi-linux-x86_64
Info: Built Mon May 9 10:46:23 CDT 2016 by tg804216 on login2.stampede.tacc.utexas.edu
Info: 1 NAMD  2.11  Linux-x86_64-MPI  16    c560-701.stampede.tacc.utexas.edu  tg804216
Info: Running on 16 processors, 16 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0320759 s
Info: 263.52 MB of memory in use based on /proc/self/stat
Info: Configuration file is FEP01.conf
Info: Working in the current directory /scratch/01143/tg804216/proj8/SimsInputs/3D4S/test_namd_mailing_list2
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE   eq9.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        20
Info: PERIODIC CELL BASIS 1  81.2352 0 0
Info: PERIODIC CELL BASIS 2  0 80.2855 0
Info: PERIODIC CELL BASIS 3  0 0 101.861
Info: PERIODIC CELL CENTER   0 0 0
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER  Centralized
Info: LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT
Info: LDB PERIOD             4000 steps
Info: FIRST LDB TIMESTEP     100
Info: LAST LDB TIMESTEP     -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH    40
Info: VELOCITY FILE          eq9.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME           fep01.dcd
Info: DCD FREQUENCY          2500
Info: DCD FIRST STEP         2500
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           fep01.xst
Info: XST FREQUENCY          2500
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        fep01
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       fep01.restart
Info: RESTART FREQUENCY      2500
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: VDW FORCE SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      14
Info: PAIRLIST SHRINK RATE   0.01
Info: PAIRLIST GROW RATE     0.01
Info: PAIRLIST TRIGGER       0.3
Info: PAIRLISTS PER CYCLE    2
Info: PAIRLISTS ENABLED
Info: MARGIN                 1.008
Info: HYDROGEN GROUP CUTOFF  2.8
Info: PATCH DIMENSION        17.808
Info: ENERGY OUTPUT STEPS    10
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    2500
Info: THERMODYNAMIC INTEGRATION (TI) ON
Info: TI LAMBDA VALUE     0
Info: TI INTRA-ALCHEMICAL NON-BONDED INTERACTIONS WILL BE RETAINED
Info: TI INTRA-ALCHEMICAL BONDED INTERACTIONS WILL BE RETAINED
Info: TI VDW SHIFTING COEFFICIENT 6
Info: TI ELEC. ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 0.5
Info: TI ELEC. ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0.5 AND LAMBDA = 1
Info: TI VDW ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0.5 AND LAMBDA = 1
Info: TI VDW ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 0.5
Info: TI BOND ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 1
Info: TI BOND ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 1
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   300
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 0.1 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info:        TARGET PRESSURE IS 1 BAR
Info:     OSCILLATION PERIOD IS 200 FS
Info:             DECAY TIME IS 100 FS
Info:     PISTON TEMPERATURE IS 300 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS 2.03684e-05 2.03684e-05 -4.36381e-07
Info:       CELL FLUCTUATION IS ANISOTROPIC
Info:     SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE               1e-06
Info: PME EWALD COEFFICIENT       0.257952
Info: PME INTERPOLATION ORDER     6
Info: PME GRID DIMENSIONS         84 84 108
Info: PME MAXIMUM GRID SPACING    1
Info: Attempting to read FFTW data from FFTW_NAMD_2.11_Linux-x86_64-MPI.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.11_Linux-x86_64-MPI.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      2
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info:         ERROR TOLERANCE : 1e-08
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED     1463511698
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         ../out7_ions.pdb
Info: STRUCTURE FILE         ../out7_ions.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             ../../toppar/par_all36_prot.prm
Info: PARAMETERS             ../../toppar/par_all36_na.prm
Info: PARAMETERS             ../../toppar/par_all36_carb.prm
Info: PARAMETERS             ../../toppar/par_all36_lipid.prm
Info: PARAMETERS             ../../toppar/par_all36_cgenff.prm
Info: PARAMETERS             ../../toppar/chol.prm
Info: PARAMETERS             ../../toppar/wation.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES     eq9.coor
Warning: SKIPPING PART OF PARAMETER FILE AFTER RETURN STATEMENT
Info: SUMMARY OF PARAMETERS:
Info: 939 BONDS
Info: 2773 ANGLES
Info: 6799 DIHEDRAL
Info: 193 IMPROPER
Info: 6 CROSSTERM
Info: 350 VDW
Info: 23 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 7.76219
Info: Reading pdb file ../out7_ions.pdb
Info: TIME FOR READING PDB FILE: 0.182948
Info: 
Info: To read alchdata from file: ../out9_alchfile.pdb
Info: To read alchflag data from column: 5
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 69634 ATOMS
Info: 56966 BONDS
Info: 73525 ANGLES
Info: 88042 DIHEDRALS
Info: 1032 IMPROPERS
Info: 275 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 56919 RIGID BONDS
Info: ALCH: 74 ATOMS TO DISAPPEAR IN FINAL STATE
Info: ALCH: 0 ATOMS TO APPEAR IN FINAL STATE
Info: 151983 DEGREES OF FREEDOM
Info: 25417 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 25417 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 413314 amu
Info: TOTAL CHARGE = 9.818e-06 e
Info: MASS DENSITY = 1.03312 g/cm^3
Info: ATOM DENSITY = 0.104817 atoms/A^3
Info: *****************************
Info: Reading from binary file eq9.coor
Info: 
Info: Entering startup at 8.83804 s, 388.672 MB of memory in use
Info: Startup phase 0 took 0.000277996 s, 388.672 MB of memory in use
Info: ADDED 217340 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.0927439 s, 399.961 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.6778e-33 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 3.71539e-17 AT 11.9974
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 9.34011e-27 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 2.98256e-17 AT 11.9974
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.00525713 s, 403.703 MB of memory in use
Info: Startup phase 3 took 0.000169039 s, 403.703 MB of memory in use
Info: Startup phase 4 took 0.000413895 s, 403.703 MB of memory in use
Info: Startup phase 5 took 0.000139952 s, 403.703 MB of memory in use
Info: PATCH GRID IS 4 (PERIODIC) BY 4 (PERIODIC) BY 5 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file eq9.vel
Info: REMOVING COM VELOCITY 0.00634616 0.00950085 -0.00831659
Info: LARGEST PATCH (53) HAS 953 ATOMS
Info: TORUS A SIZE 16 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.043546 s, 419.773 MB of memory in use
Info: PME using 14 and 14 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 9 10 11 ...
Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
Info: PME USING 14 GRID NODES AND 14 TRANS NODES
Info: Startup phase 7 took 0.00420523 s, 419.773 MB of memory in use
Info: Startup phase 8 took 0.00143886 s, 419.773 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.00159097 s, 419.773 MB of memory in use
Info: CREATING 1680 COMPUTE OBJECTS
Info: Startup phase 10 took 0.00376916 s, 419.773 MB of memory in use
Info: useSync: 0 useProxySync: 0
Info: Startup phase 11 took 0.000248909 s, 419.773 MB of memory in use
Info: Startup phase 12 took 0.000320911 s, 419.773 MB of memory in use
Info: Finished startup at 8.99217 s, 419.773 MB of memory in use

TCL: Running for 1000000 steps
TI: RESETTING FOR NEW WINDOW LAMBDA SET TO 0
TI: WINDOW TO HAVE 300000 STEPS OF EQUILIBRATION PRIOR TO TI DATA COLLECTION.
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG               BOND1         ELECT1           VDW1          BOND2         ELECT2                VDW2

ENERGY:       0      3890.8379     19121.1035     12892.7708       231.7270        -173040.0543      3646.2544         0.0000         0.0000     45249.3689         -88007.9917       299.6456   -133257.3606    -87684.2150       299.6456             94.2039       118.9193    664336.2988        94.2039       118.9193              0.0000         0.0000         0.0000         0.0000       -21.5365              1.1366

OPENING TI ENERGY OUTPUT FILE
OPENING EXTENDED SYSTEM TRAJECTORY FILE
ENERGY:      10      3966.2325     19220.5987     12903.2921       233.3596        -172809.6355      3266.1059         0.0000         0.0000     45203.0688         -88016.9778       299.3390   -133220.0466    -87694.0401       298.8748           -205.3403      -185.6723    665146.0281      -160.9289      -162.3131              0.0000         0.0000         0.0000         0.0000       -21.3574            -12.1578

LDB: ============= START OF LOAD BALANCING ============== 10.6973
LDB: ============== END OF LOAD BALANCING =============== 10.6985
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 10.6989
ENERGY:      20      3977.1971     19177.4445     12887.7331       228.8157        -172707.7978      3261.7947         0.0000         0.0000     45147.3367         -88027.4760       298.9699   -133174.8127    -87705.8494       298.9333           -383.3062      -367.9792    665430.8026       -10.1143        -8.9289              0.0000         0.0000         0.0000         0.0000       -19.8677             -2.9351

ENERGY:      30      3957.2985     19278.4299     12874.1209       235.2634        -173001.6369      3696.6836         0.0000         0.0000     44955.2082         -88004.6325       297.6976   -132959.8407    -87679.9922       298.5863            250.7778       273.1307    664395.3954       113.8264       114.1146              0.0000         0.0000         0.0000         0.0000       -20.7426             -2.4965

ENERGY:      40      4022.0583     19200.3981     12901.5876       230.6527        -172932.9668      3522.4791         0.0000         0.0000     45043.5532         -88012.2378       298.2827   -133055.7910    -87693.2913       298.4461              6.9615        31.2499    664702.1148       -86.8505       -87.1546              0.0000         0.0000         0.0000         0.0000       -18.9707              8.4701

ENERGY:      50      3967.4185     19166.5142     12855.1321       223.7503        -173196.0890      3743.5310         0.0000         0.0000     45202.7217         -88037.0212       299.3367   -133239.7429    -87718.7213       299.2255            -44.9759       -27.4238    664478.4282        37.8541        36.4068              0.0000         0.0000         0.0000         0.0000       -15.5725             11.4432

ENERGY:      60      4026.6255     19075.9474     12948.3594       227.8657        -173374.3533      3732.8950         0.0000         0.0000     45321.1801         -88041.4802       300.1211   -133362.6602    -87719.7301       299.6455             62.4418        82.8662    664089.8181        73.7610        73.4222              0.0000         0.0000         0.0000         0.0000       -17.5810             36.4834

ENERGY:      70      4014.0142     19180.4266     12903.5920       236.6909        -173179.8165      3564.7065         0.0000         0.0000     45233.0496         -88047.3368       299.5375   -133280.3864    -87720.4378       299.6492           -196.8710      -176.8780    664277.9546        83.8444        85.9153              0.0000         0.0000         0.0000         0.0000       -19.8908             34.8376

ENERGY:      80      3983.6894     19136.3943     12964.9312       233.0626        -173411.6914      3890.7885         0.0000         0.0000     45149.0270         -88053.7984       298.9811   -133202.8254    -87734.5782       299.3338            309.0318       326.5163    663189.7165       -67.4250       -67.5659              0.0000         0.0000         0.0000         0.0000       -17.7613              9.0456

ENERGY:      90      3976.1552     19129.3678     12961.3366       235.5519        -173131.6078      3651.1012         0.0000         0.0000     45151.4370         -88026.6581       298.9971   -133178.0951    -87701.2958       298.8258           -133.4697      -119.7486    663343.5381        79.2592        81.1907              0.0000         0.0000         0.0000         0.0000       -19.6168             -8.9447

LDB: ============= START OF LOAD BALANCING ============== 17.4444
LDB: Largest compute 143 load 0.289016 is 4.6% of average load 6.323856
LDB: Average compute 0.036023 is 0.6% of average load 6.323856
LDB: Partitioning computes with target load 0.632386
LDB: Increased migratable compute count from 1520 to 1520
LDB: Largest unpartitionable compute is 0.040061
LDB: ============== END OF LOAD BALANCING =============== 17.4462
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 17.4472
Info: Initial time: 16 CPUs 0.0842923 s/step 0.487803 days/ns 428.699 MB memory
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG               BOND1         ELECT1           VDW1          BOND2         ELECT2                VDW2

ENERGY:     100      4034.2236     19108.1775     12924.5489       240.0672        -173209.1904      3555.8572         0.0000         0.0000     45349.4693         -87996.8467       300.3085   -133346.3160    -87673.0087       300.1758             18.5107        38.0175    663033.6708        51.3273        52.0089              0.0000         0.0000         0.0000         0.0000       -21.6713            -10.2456

ENERGY:     110      3969.4477     19199.9544     12945.6267       215.2822        -173044.5462      3609.0205         0.0000         0.0000     45137.0135         -87968.2012       298.9016   -133105.2147    -87644.8748       299.5695             63.9752        90.0367    663313.6059        29.3263        29.6001              0.0000         0.0000         0.0000         0.0000       -25.8513             12.0681

LDB: ============= START OF LOAD BALANCING ============== 19.137
LDB: ============== END OF LOAD BALANCING =============== 19.1372
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 19.1377
ENERGY:     120      3919.8877     19307.3529     12944.1863       229.8404        -172608.9279      3139.2070         0.0000         0.0000     45097.6025         -87970.8511       298.6406   -133068.4536    -87647.6920       298.7221           -236.7842      -215.5863    664112.1123       -39.5691       -38.7873              0.0000         0.0000         0.0000         0.0000       -24.7643             34.1586

ENERGY:     130      3974.9090     18977.0820     12950.1006       220.2203        -172721.6321      3386.2583         0.0000         0.0000     45258.7122         -87954.3498       299.7075   -133213.0620    -87617.9020       298.6873             83.2825       108.3377    663344.5012        -2.0035        -1.4585              0.0000         0.0000         0.0000         0.0000       -25.8590             38.4895

ENERGY:     140      3902.9137     18968.4434     12973.1921       214.2248        -172937.3980      3512.3737         0.0000         0.0000     45411.8386         -87954.4118       300.7215   -133366.2504    -87630.1046       299.2219             87.6515       105.2759    662962.0374       128.4899       127.6998              0.0000         0.0000         0.0000         0.0000       -23.4049              0.4082

ENERGY:     150      3984.5539     19171.4767     12973.6548       238.5272        -172622.8798      3322.4317         0.0000         0.0000     44978.4632         -87953.7723       297.8516   -132932.2355    -87632.9224       299.2150             34.4868        58.4000    663766.1786       -29.5294       -29.7744              0.0000         0.0000         0.0000         0.0000       -23.1702             20.3297

ENERGY:     160      3980.0411     19162.2648     12923.5877       230.7387        -172671.3937      3425.7590         0.0000         0.0000     44988.4562         -87960.5462       297.9178   -132949.0024    -87639.9257       298.4993           -232.1499      -208.9489    664408.7800       -66.0533       -64.7445              0.0000         0.0000         0.0000         0.0000       -20.2777            -12.2677

ENERGY:     170      3948.0286     19082.9258     12861.0369       228.2407        -173027.1432      3677.3043         0.0000         0.0000     45251.5320         -87978.0748       299.6599   -133229.6068    -87654.1328       298.6818            150.8222       172.6240    663812.5559        24.8747        25.8228              0.0000         0.0000         0.0000         0.0000       -21.2916             20.9409

ENERGY:     180      3939.8009     19126.5726     12901.9926       251.2721        -173135.7681      3693.2504         0.0000         0.0000     45244.5498         -87978.3298       299.6137   -133222.8795    -87657.5101       299.7677            180.5959       201.6947    663689.9557       -18.5817       -19.8035              0.0000         0.0000         0.0000         0.0000       -22.1347             25.4082

ENERGY:     190      3993.9502     19120.2041     12897.4263       244.4814        -172996.3958      3397.5600         0.0000         0.0000     45367.2861         -87975.4877       300.4265   -133342.7738    -87648.8639       300.2045           -330.8113      -305.9741    664609.3798       101.7889       101.3672              0.0000         0.0000         0.0000         0.0000       -20.6841             29.8658

LDB: ============= START OF LOAD BALANCING ============== 25.9881
LDB: Largest compute 143 load 0.293845 is 4.6% of average load 6.412930
LDB: Average compute 0.036174 is 0.6% of average load 6.412930
LDB: TIME 25.989 LOAD: AVG 6.41293 MAX 6.6211  PROXIES: TOTAL 240 MAXPE 15 MAXPATCH 3 None MEM: 429.594 MB
LDB: TIME 25.9899 LOAD: AVG 6.41293 MAX 6.4462  PROXIES: TOTAL 240 MAXPE 15 MAXPATCH 3 TorusLB MEM: 429.594 MB
LDB: ============== END OF LOAD BALANCING =============== 25.9908
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 25.9922
Info: Initial time: 16 CPUs 0.0853037 s/step 0.493655 days/ns 431.473 MB memory
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG               BOND1         ELECT1           VDW1          BOND2         ELECT2                VDW2

ENERGY:     200      4011.7142     19123.3065     12900.3004       226.0864        -172965.6436      3421.7653         0.0000         0.0000     45307.1947         -87975.2761       300.0285   -133282.4708    -87650.6858       299.9890           -133.9797      -107.5224    665069.5287       -46.2656       -46.7410              0.0000         0.0000         0.0000         0.0000       -21.4175             -0.7341

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