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mattwthompson/mdout

Created June 13, 2023 20:11
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mdout
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mdout
-------------------------------------------------------
Amber 22 SANDER 2022
-------------------------------------------------------
| Run on 06/13/2023 at 15:09:44
| Executable path: sander
| Working directory: /Users/mattthompson/software/openff-interchange
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: run.in
| MDOUT: out.mdout
|INPCRD: out.inpcrd
| PARM: out.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
Here is the input file:
single-point energy
&cntrl
imin=1,
maxcyc=0,
ntb=1,
fswitch=8.0,
ntc=1,
ntf=1,
cut=9.0,
/
&ewald
order=4
skinnb=1.0
//
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 25.000
| New format PARM file being parsed.
| Version = 1.000 Date = 06/13/23 Time = 15:09:44
NATOM = 9 NTYPES = 5 NBONH = 4 MBONA = 5
NTHETH = 8 MTHETA = 5 NPHIH = 23 MPHIA = 5
NHPARM = 0 NPARM = 0 NNB = 35 NRES = 1
NBONA = 5 NTHETA = 5 NPHIA = 5 NUMBND = 6
NUMANG = 5 NPTRA = 8 NATYP = 1 NPHB = 0
IFBOX = 1 NMXRS = 9 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 785218
| Hollerith 30
| Integer 21568
| Max Pairs 36
| nblistReal 108
| nblist Int 321577
| Total 7476 kbytes
| 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
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 50, ntrx = 1, ntwr = 1
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 0, eedmeth = 1, netfrc = 0
Box X = 50.000 Box Y = 50.000 Box Z = 50.000
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 50 NFFT2 = 50 NFFT3 = 50
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
--------------------------------------------------------------------------------
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
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 3
| TOTAL SIZE OF NONBOND LIST = 3
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.9627E+01 2.3061E+01 8.1310E+01 C1 2
BOND = 4.4502 ANGLE = 28.3399 DIHED = 0.0000
VDWAALS = -0.0045 EEL = 2.0114 HBOND = 0.0000
1-4 VDW = -0.1376 1-4 EEL = -5.0320 RESTRAINT = 0.0000
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.9627E+01 2.3061E+01 8.1310E+01 C1 2
BOND = 4.4502 ANGLE = 28.3399 DIHED = 0.0000
VDWAALS = -0.0045 EEL = 2.0114 HBOND = 0.0000
1-4 VDW = -0.1376 1-4 EEL = -5.0320 RESTRAINT = 0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 0.55% of Total)
| Fast Water setup 0.00 ( 0.12% of Total)
| Build the list 0.00 (17.20% of List )
| Other 0.00 (82.80% of List )
| List time 0.00 (35.83% of Nonbo)
| Direct Ewald time 0.00 ( 0.18% of Ewald)
| Adjust Ewald time 0.00 ( 0.02% of Ewald)
| Self Ewald time 0.00 ( 0.04% of Ewald)
| Fill Bspline coeffs 0.00 ( 0.55% of Recip)
| Fill charge grid 0.00 ( 3.87% of Recip)
| Scalar sum 0.00 (21.23% of Recip)
| Grad sum 0.00 ( 0.07% of Recip)
| FFT time 0.01 (72.67% of Recip)
| Other 0.00 ( 1.61% of Recip)
| Recip Ewald time 0.01 (97.04% of Ewald)
| Virial junk 0.00 ( 0.03% of Ewald)
| Other 0.00 ( 2.69% of Ewald)
| Ewald time 0.01 (64.17% of Nonbo)
| Nonbond force 0.01 (97.04% of Force)
| Bond/Angle/Dihedral 0.00 ( 1.80% of Force)
| Other 0.00 ( 1.16% of Force)
| Force time 0.01 (100.0% of Runmd)
| Runmd Time 0.01 (40.81% of Total)
| Other 0.02 (58.52% of Total)
| Total time 0.03 (98.57% of ALL )
| Number of list builds : 1
| Highest rstack allocated: 278665
| Highest istack allocated: 9
| Job began at 15:09:44.561 on 06/13/2023
| Setup done at 15:09:44.577 on 06/13/2023
| Run done at 15:09:44.594 on 06/13/2023
| wallclock() was called 88 times
|3D-RISM memory allocation summary
|Type Maximum Current
|Integer 0.00000 GB 0.00000 GB
|Real 0.00000 GB 0.00000 GB
|Logical 0.00000 GB 0.00000 GB
|Character 0.00000 GB 0.00000 GB
|---------------------------------------
|Total 0.00000 GB 0.00000 GB
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