Hi,
The first thing I would do is to make sure PMEMD is reading your restart
file correctly - can you post the first 3 lines of your restart file (which
should contain simulation time that the restart corresponds to among other
things)? It's possible that if the file system of the resource you were
using to run your simulation had problems during the course of the run that
your restart file was not being written correctly. Did you see any signs of
corruption in your output file or trajectory file? You can easily check how
many frames are in your trajectory with cpptraj (by my count according to
your ntwx setting you should have 1000 frames in md1.nc):
parm ionicbox.prmtop
trajin md1.nc
list trajin
quit
Also, one piece of general advice: in my opinion you're writing your
restart file *way* too frequently. I typically will choose a value that's
about 100 times less often than I write my trajectory. The main reason for
this is speed/efficiency; writing restarts tends to be time-consuming since
you need to open and close the restart file every time it's written. It
also may be better to use the NetCDF restart format (ntxo=2).
Hope this helps,
-Dan
On Mon, Jan 20, 2014 at 1:42 PM, Saeed Nasiri <s.t.nasiri.gmail.com> wrote:
> Dear all
>
> I do a MD simulation like the amber ionic liquid tutorial. for the first
> step I do for 5ns. after the md finished the job was in the queue?
> I copy the necessary file to another directory and restart MD, but the
> simulation restarting from 3186 ps not from 5000 ps?
> what could I do?
>
> best regard
> Nasiri
>
> =============================================================
> tail -100 md1.out
> Ewald error estimate: 0.1647E-04
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 4995000 TIME(PS) = 4995.000 TEMP(K) = 306.79 PRESS =
> 369.7
> Etot = 110.7584 EKtot = 2064.8800 EPtot =
> -1954.1216
> BOND = 687.2929 ANGLE = 873.1544 DIHED =
> 169.9640
> 1-4 NB = 31.6772 1-4 EEL = 945.9037 VDWAALS =
> -828.1005
> EELEC = -3834.0133 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 266.4169 VIRIAL = 76.0272 VOLUME =
> 23853.2236
> Density =
> 0.9624
> Ewald error estimate: 0.6979E-06
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 5000000 TIME(PS) = 5000.000 TEMP(K) = 300.06 PRESS =
> -135.8
> Etot = 22.0233 EKtot = 2019.5567 EPtot =
> -1997.5333
> BOND = 700.4772 ANGLE = 823.8397 DIHED =
> 173.2342
> 1-4 NB = 31.0197 1-4 EEL = 946.8374 VDWAALS =
> -869.5587
> EELEC = -3803.3828 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 300.1690 VIRIAL = 370.0495 VOLUME =
> 23840.3763
> Density =
> 0.9629
> Ewald error estimate: 0.2457E-03
>
> ------------------------------------------------------------------------------
>
>
> A V E R A G E S O V E R 5000000 S T E P S
>
>
> NSTEP = 5000000 TIME(PS) = 5000.000 TEMP(K) = 297.90 PRESS =
> -3.4
> Etot = 53.4122 EKtot = 2005.0617 EPtot =
> -1951.6496
> BOND = 698.9419 ANGLE = 869.5246 DIHED =
> 162.2404
> 1-4 NB = 31.4564 1-4 EEL = 944.0402 VDWAALS =
> -847.0310
> EELEC = -3810.8221 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 288.5973 VIRIAL = 291.9293 VOLUME =
> 24460.4248
> Density =
> 0.9503
> Ewald error estimate: 0.1498E-03
>
> ------------------------------------------------------------------------------
>
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 5000000 TIME(PS) = 5000.000 TEMP(K) = 5.15 PRESS =
> 329.5
> Etot = 77.0081 EKtot = 34.6406 EPtot =
> 68.4932
> BOND = 22.4479 ANGLE = 20.9366 DIHED =
> 8.0117
> 1-4 NB = 2.1977 1-4 EEL = 2.3697 VDWAALS =
> 44.8811
> EELEC = 39.7736 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 13.0234 VIRIAL = 172.7217 VOLUME =
> 3926.6309
> Density =
> 0.0748
> Ewald error estimate: 0.1136E-03
>
> ------------------------------------------------------------------------------
>
>
>
> --------------------------------------------------------------------------------
> 5. TIMINGS
>
> --------------------------------------------------------------------------------
>
> | Build the list 9184.60 (98.77% of List )
> | Other 114.18 ( 1.23% of List )
> | List time 9298.78 ( 2.54% of Nonbo)
> | Short_ene time 312434.00 (99.71% of Direc)
> | Other 896.26 ( 0.29% of Direc)
> | Direct Ewald time 313330.26 (87.85% of Ewald)
> | Adjust Ewald time 2853.11 ( 0.80% of Ewald)
> | Fill Bspline coeffs 1530.58 ( 3.85% of Recip)
> | Fill charge grid 3737.07 ( 9.41% of Recip)
> | Scalar sum 10494.56 (26.43% of Recip)
> | Grad sum 5608.26 (14.12% of Recip)
> | FFT time 18329.08 (46.16% of Recip)
> | Other 9.62 ( 0.02% of Recip)
> | Recip Ewald time 39709.17 (11.13% of Ewald)
> | Force Adjust 31.91 ( 0.01% of Ewald)
> | Virial junk 122.55 ( 0.03% of Ewald)
> | Other 600.28 ( 0.17% of Ewald)
> | Ewald time 356660.13 (97.46% of Nonbo)
> | Nonbond force 365965.32 (99.01% of Force)
> | Bond/Angle/Dihedral 3621.94 ( 0.98% of Force)
> | Other 54.67 ( 0.01% of Force)
> | Force time 369641.92 (98.08% of Runmd)
> | Verlet update time 7083.53 ( 1.88% of Runmd)
> | Ekcmr time 96.58 ( 0.03% of Runmd)
> | Other 42.96 ( 0.01% of Runmd)
> | Runmd Time 376865.00 (100.0% of Total)
> | Total time 376865.15 (100.0% of ALL )
>
> | Highest rstack allocated: 207308
> | Highest istack allocated: 2258
>
> | Final Performance Info:
> | -----------------------------------------------------
> | Average timings for all steps:
> | Elapsed(s) = 376865.00 Per Step(ms) = 75.37
> | ns/day = 1.15 seconds/ns = 75373.00
> | -----------------------------------------------------
>
> | Job began at 14:47:17.472 on 01/16/2014
> | Setup done at 14:47:17.623 on 01/16/2014
> | Run done at 23:28:22.624 on 01/20/2014
> | wallclock() was called******** times
>
> =============================================================
>
> tail -200 md2.out
>
> -------------------------------------------------------
> Amber 12 SANDER 2012
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 12
>
> | Run on 01/20/2014 at 22:58:47
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: mdin.in
>
> | MDOUT:
> md2.out
> | INPCRD:
> md1.x
> | PARM:
> ionicbox.prmtop
> | RESTRT:
> md2.x
> | REFC:
> refc
> | MDVEL:
> mdvel
> | MDEN:
> md2.dat
> | MDCRD: md2.nc
>
> | MDINFO:
> mdinfo
>
>
> Here is the input file:
>
> equilibration for
> box
> &cntrl
>
> imin=0, ntpr=5000,
> ntwx=5000,
> ntx=5,
> irest=1,
> tempi=298., temp0=298., ntt=3,
> cut=12,
> gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1,
> nstlim=5000000,
> ntwr=1000, dt=.001,
> ig=-1,
> &end
>
>
>
> Note: ig = -1. Setting random seed based on wallclock time in microseconds.
>
>
> | Conditional Compilation Defines Used:
> | DIRFRC_COMTRANS
> | DIRFRC_EFS
> | DIRFRC_NOVEC
> | PUBFFT
> | FFTLOADBAL_2PROC
> | BINTRAJ
>
> | Largest sphere to fit in unit cell has radius = 14.297
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 01/01/14 Time = 16:48:05
>
> | 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 = 2258 NTYPES = 10 NBONH = 1454 MBONA = 501
> NTHETH = 2693 MTHETA = 264 NPHIH = 1921 MPHIA = 374
> NHPARM = 0 NPARM = 0 NNB = 7356 NRES = 325
> NBONA = 501 NTHETA = 264 NPHIA = 374 NUMBND = 12
> NUMANG = 21 NPTRA = 11 NATYP = 11 NPHB = 0
> IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> | Coordinate Index Table dimensions: 4 4 4
> | Direct force subcell size = 7.1813 7.1813 7.1486
>
> 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 = 5000, ntrx = 1, ntwr =
> 1000
> iwrap = 0, ntwx = 5000, ntwv = 0, ntwe
> = 0
> ioutfm = 1, ntwprt = 0, idecomp = 0,
> rbornstat= 0
>
> Potential function:
> ntf = 1, 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 = 5000000, nscm = 1000, nrespa = 1
> t = 0.00000, dt = 0.00100, vlimit = 20.00000
>
> Langevin dynamics temperature regulation:
> ig = 986688
> temp0 = 298.00000, tempi = 298.00000, gamma_ln= 5.00000
>
> Pressure regulation:
> ntp = 1
> pres0 = 1.00000, comp = 44.60000, taup = 1.00000
>
> | Intermolecular bonds treatment:
> | no_intermolecular_bonds = 1
>
> | Energy averages sample interval:
> | ene_avg_sampling = 5000
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme
> = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 1
> Box X = 28.725 Box Y = 28.725 Box Z = 28.594
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 30 NFFT2 = 30 NFFT3 = 30
> Cutoff= 12.000 Tol =0.100E-04
> Ewald Coefficient = 0.22664
> Interpolation order = 4
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
> default_name
>
> begin time read from input coords = 3181.000 ps
>
>
> Number of triangulated 3-point waters found: 0
>
> Sum of charges from parm topology file = -0.00004337
> Forcing neutrality...
>
> | Dynamic Memory, Types Used:
> | Reals 233496
> | Integers 120508
>
> | Nonbonded Pairs Initial Allocation: 1122959
>
>
> --------------------------------------------------------------------------------
> 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 = 5000 TIME(PS) = 3186.000 TEMP(K) = 298.89 PRESS =
> -383.5
> Etot = 72.3120 EKtot = 2011.7339 EPtot =
> -1939.4220
> BOND = 684.8586 ANGLE = 887.5292 DIHED =
> 172.0031
> 1-4 NB = 29.7509 1-4 EEL = 947.8695 VDWAALS =
> -881.9305
> EELEC = -3779.5029 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 297.6092 VIRIAL = 493.6856 VOLUME =
> 23677.4832
> Density =
> 0.9695
> Ewald error estimate: 0.1282E-03
>
> ------------------------------------------------------------------------------
> =============================================================
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jan 20 2014 - 17:30:02 PST
