1) have you run md with all of these settings except for smd?
2) it looks like the initial restraint energy is high, is that expected?
You might want your initial target to be that same as in the inout
coordinates.
On Mon, Jan 17, 2022, 11:33 AM natalia francisca rodriguez cabello <
nrodriguez13.alumnos.utalca.cl> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 17 2022 - 10:00:02 PST
