Hi,
I must perform SMD. Previously I had done the calculation in GPU and it failed, I tried a small calculation in CPU and it worked but now it crashes again. (I already did minimization and DM for the system finishing fine). I also tried modifying imin=0,
irest=1,
ntx=5 Unsuccessfully.
The output is as follows:
Here is the input file:
A NPT simulation for common production-level simulations
&cntrl
imin=0, ! No minimization
irest=0, ! This IS a restart of an old MD simulation
ntx=1, ! So our inpcrd file has velocities
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
temp0=310, ! Target temperature
! Potential energy control
cut=12.0, ! nonbonded cutoff, in Angstroms
fswitch=10.0, ! Force-based switching
! MD settings
nstlim=1625000, ! 500K steps, 1 ns total
dt=0.002, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=2, ! Do not calculate forces of bonds containing hydrogen
! Control how often information is printed
ntpr=1000, ! Print energies every 1000 steps
ntwx=1000, ! Print coordinates every 50000 steps to the trajectory
ntwr=1000, ! Print a restart file every 10K steps (can be less frequent)
! ntwv=-1, ! Uncomment to also print velocities to trajectory
! ntwf=-1, ! Uncomment to also print forces to trajectory
ntxo=2, ! Write NetCDF format
ioutfm=1, ! Write NetCDF format (always do this!)
! Wrap coordinates when printing them to the same unit cell
iwrap=1,
! Constant pressure control.
barostat=2, ! MC barostat... change to 1 for Berendsen
ntp=1, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
pres0=1.0, ! Target external pressure, in bar
nmropt=1,
jar=1,
ig=-1,
! Set water atom/residue names for SETTLE recognition
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
/
&wt type='DUMPFREQ', istep1=1000 /
&wt type='END', /
DISANG=COM_PULL.RST
DUMPAVE=Pull_dist.dat
LISTIN=POUT
LISTOUT=POUT
/
/
&ewald
vdwmeth = 0,
/
Note: ig = -1. Setting random seed to 292388 based on wallclock time in
microseconds.
| irandom = 1, using AMBER's internal random number generator (default).
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| EMIL
| Largest sphere to fit in unit cell has radius = 52.076
| New format PARM file being parsed.
| Version = 1.000 Date = 01/11/22 Time = 10:59:15
| Force field information read from topology file:
| CHARMM:
|
|CHARMM: CHARMM force field in use.
| 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.
| INFO: Off Diagonal (NBFIX) LJ terms found in prmtop file.
| The prmtop file has been modified to support atom
| type based pairwise Lennard-Jones terms.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting box info from netcdf restart file
NATOM = 118212 NTYPES = 27 NBONH = 117448 MBONA = 514
NTHETH = 40488 MTHETA = 614 NPHIH = 2330 MPHIA = 1084
NHPARM = 0 NPARM = 0 NNB = 162387 NRES = 39244
NBONA = 514 NTHETA = 614 NPHIA = 1084 NUMBND = 33
NUMANG = 60 NPTRA = 101 NATYP = 1 NPHB = 0
IFBOX = 1 NMXRS = 46 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 16 16 16
| Direct force subcell size = 6.6155 6.5095 6.7052
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 1000, ntrx = 1, ntwr = 1000
iwrap = 1, ntwx = 1000, 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 = 12.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 1625000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 292388
temp0 = 310.00000, tempi = 0.00000, gamma_ln= 1.00000
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
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 0, eedmeth = 1, netfrc = 1
Box X = 105.848 Box Y = 104.152 Box Z = 107.283
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 108 NFFT2 = 108 NFFT3 = 108
Cutoff= 12.000 Tol =0.100E-04
Ewald Coefficient = 0.22664
Interpolation order = 4
| MONTE CARLO BAROSTAT IMPORTANT NOTE:
| The Monte-Carlo barostat does not require the virial to adjust the system volume.
| Since it is an expensive calculation, it is skipped for efficiency. A side-effect
| is that the reported pressure is always 0 because it is not calculated.
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 1000.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
DUMPFREQ 1000 0 0.000000 0.000000 0 0
** No weight changes given **
RESTRAINTS:
Requested file redirections:
DISANG = COM_PULL.RST
DUMPAVE = Pull_dist.dat
LISTIN = POUT
LISTOUT = POUT
Restraints will be read from file: COM_PULL.RST
Here are comments from the DISANG input file:
jar option running
******
COM ( -1)-COM ( -1) NSTEP1= 0 NSTEP2=******
Atom ranges defining Center of Mass Group in the first position:
1 -> 1/ 4 -> 5/ 8 -> 8/
Atom ranges defining Center of Mass Group in the second position:
1125 -> 1150/ 1152 -> 1153/
R1 = -87.000 R2 = 13.000 R3 = 13.000 R4 = 113.000 RK2 = 10.000 RK3 = 10.000
R1A= -99.000 R2A= 1.000 R3A= 1.000 R4A= 101.000 RK2A= 10.000 RK3A= 10.000
Rcurr: 138.302 Rcurr-(R2+R3)/2: 125.302 MIN(Rcurr-R2,Rcurr-R3): 125.302
Number of restraints read = 1
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 38930
Sum of charges from parm topology file = 0.00009600
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 4779736
| Integers 3530762
| Nonbonded Pairs Initial Allocation: 58789782
--------------------------------------------------------------------------------
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 = 0.7967E-11 at 2.716640
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.27
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.78
|---------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -250215.7880 EKtot = 0.0000 EPtot = -250215.7880
BOND = 193.6469 ANGLE = 551.6633 DIHED = 303.8936
UB = 97.2722 IMP = 17.5798 CMAP = 0.0000
1-4 NB = 135.8752 1-4 EEL = 267.0181 VDWAALS = 41700.5301
EELEC = -444086.6313 EHBOND = 0.0000 RESTRAINT = 150603.3642
EAMBER (non-restraint) = -400819.1521
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1182720.8629
Density = 1.0056
Ewald error estimate: 0.3686E-04
------------------------------------------------------------------------------
NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 9; vmax = 56.5618
vlimit exceeded for step 10; vmax = 27.1689
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 3 22 40 41
----------------------------------------
Francisca Rodríguez Cabello
Estudiante Ingeniería Civil en Bioinformática
Universidad de Talca, Chile
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Received on Mon Jan 17 2022 - 09:00:02 PST
