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logFile
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 14
| Run on 08/22/2015 at 08:35:26
| Executable path: pmemd.cuda
| Working directory: /primary/home/parker.dewaal/simulations/5HT1b/20150821_235819-Sim1-071915/prod
| Hostname: node003
[-O]verwriting output
File Assignments:
| MDIN: prod1.in
| MDOUT: prod_1.out
| INPCRD: ../eq/pressure/pressure_4.rst
| PARM: ../build/system/071915.prmtop
| RESTRT: prod_1.rst
| REFC: ../eq/minimization/min_system.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: prod_1.nc
| MDINFO: prod_1.mdinfo
| MDFRC: mdfrc
Here is the input file:
Production with MC barostat
&cntrl
irest=1, ntx =5,
nstlim=5000000, dt=0.002,
ntpr=4000, ntwr=4000, ntwx=4000,
temp0=310.0,
ntt=3, gamma_ln=5, ntb=2, ntp=1, barostat=2,
ntc=2, ntf=2, ig=-1,
cut=10,
ioutfm = 1,
iwrap=1,
/
Note: ig = -1. Setting random seed to 415547 based on wallclock time in
microseconds.
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 14.0.1
|
| 06/20/2014
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------
|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2013, 9 (9), pp3878-3888,
| DOI: 10.1021/ct400314y.
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: 0
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla K80
| CUDA Device Global Mem Size: 11519 MB
| CUDA Device Num Multiprocessors: 13
| CUDA Device Core Freq: 0.82 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 35.370
| New format PARM file being parsed.
| Version = 1.000 Date = 08/21/15 Time = 23:58:35
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 104632 NTYPES = 25 NBONH = 88335 MBONA = 16078
NTHETH = 53538 MTHETA = 19711 NPHIH = 90993 MPHIA = 62275
NHPARM = 0 NPARM = 0 NNB = 303803 NRES = 23348
NBONA = 16078 NTHETA = 19711 NPHIA = 62275 NUMBND = 111
NUMANG = 246 NPTRA = 281 NATYP = 70 NPHB = 1
IFBOX = 1 NMXRS = 79 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 21 12 22
| Direct force subcell size = 5.5145 5.8950 5.6707
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 4000, ntrx = 1, ntwr = 4000
iwrap = 1, ntwx = 4000, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
nstlim = 5000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 415547
temp0 = 310.00000, tempi = 0.00000, gamma_ln= 5.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
Monte-Carlo Barostat:
mcbarint = 100
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 4000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 115.804 Box Y = 70.740 Box Z = 124.756
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 120 NFFT2 = 72 NFFT3 = 128
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 1250.000 ps
Number of triangulated 3-point waters found: 21917
Sum of charges from parm topology file = -0.00288137
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 4061629
| Integers 6019117
| Nonbonded Pairs Initial Allocation: 31648564
| GPU memory information (estimate):
| KB of GPU memory in use: 620783
| KB of CPU memory in use: 133613
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.33
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.80
|---------------------------------------------------
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| MC Barostat: Decreasing size of volume moves
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| MC Barostat: Decreasing size of volume moves
NSTEP = 4000 TIME(PS) = 1258.000 TEMP(K) = 309.04 PRESS = 0.0
Etot = -181072.3932 EKtot = 69261.7109 EPtot = -250334.1041
BOND = 8169.2721 ANGLE = 20800.5195 DIHED = 17456.5110
1-4 NB = 5616.5985 1-4 EEL = 22234.2571 VDWAALS = 13256.8112
EELEC = -337868.0735 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1022390.5991
Density = 1.0280
------------------------------------------------------------------------------
....
skipping steps until right before crash
...
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Succeeded
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
| Attempting MC barostat change: Failed
NSTEP = 1072000 TIME(PS) = 3394.000 TEMP(K) = 310.07 PRESS = 0.0
Etot = -181587.2026 EKtot = 69492.3750 EPtot = -251079.5776
BOND = 8209.7109 ANGLE = 20663.8590 DIHED = 17290.7506
1-4 NB = 5552.3164 1-4 EEL = 22478.4357 VDWAALS = 14117.9650
EELEC = -339392.6151 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1022489.9599
Density = 1.0279
------------------------------------------------------------------------------
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