[AMBER] Need help with SMD

From: natalia francisca rodriguez cabello <nrodriguez13.alumnos.utalca.cl>
Date: Mon, 17 Jan 2022 16:33:31 +0000

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
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