[gmx-users] countinuation run problem

[Anthony Cruz]

HI:
Yesterday one of my simulation crash. I check the log file. This are the last 
lines of the file:

Step           Time         Lambda
        6109000    12218.00098        0.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.058792   1139   1140   0.007195
        After LINCS         0.000126     75     77   0.000021

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    3.95784e+03    1.69609e+03    1.21916e+03    7.85820e+02    3.20988e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)      Potential
    2.49591e+05   -7.40570e+03   -1.58839e+06   -2.16905e+05   -1.52336e+06
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    2.74080e+05   -1.24927e+06    2.97765e+02   -8.69934e+00

Then I try to use tpbconvert to continue the simulation by the following 
command:

-bash-2.05b$ tpbconv -f 1scnMD_MV.trr -e 1scn_MD_ENER.edr -s 1scn_MD_TPR.tpr 
-o 1scn_MD_TPR_CONT.tpr
                         :-)  G  R  O  M  A  C  S  (-:

                               Grunge ROck MAChoS

                            :-)  VERSION 3.2.1  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2004, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                               :-)  tpbconv  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -s 1scn_MD_TPR.tpr  Input        Generic run input: tpr tpb tpa xml
  -f  1scnMD_MV.trr  Input, Opt!  Full precision trajectory: trr trj
  -e 1scn_MD_ENER.edr  Input, Opt!  Generic energy: edr ene
  -n      index.ndx  Input, Opt.  Index file
  -o 1scn_MD_TPR_CONT.tpr  Output       Generic run input: tpr tpb tpa xml

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int      0  Set the nicelevel
       -time   real     -1  Continue from frame at this time (ps) instead of
                            the last frame
     -extend   real      0  Extend runtime by this amount (ps)
      -until   real      0  Extend runtime until this ending time (ps)
  -[no]zeroq   bool     no  Set the charges of a group (from the index) to
                            zero
-[no]unconstrained
               bool    yes  For a continuous trajectory, the constraints
                            should not be solved before the first step
                            (default)

Reading toplogy and shit from 1scn_MD_TPR.tpr
Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
Modifying ir->bUncStart to TRUE

READING COORDS, VELS AND BOX FROM TRAJECTORY 1scnMD_MV.trr...

trn version: GMX_trn_file (single precision)
Read frame   2334: step 1166500 time 2333.000

Using frame of step 1166500 time 2333
Opened 1scn_MD_ENER.edr as single precision energy file
Reading frame   2330 time 2330.000

READ 3 PRESSURE COUPLING MU'S FROM 1scn_MD_ENER.edr


READ 4 TEMPERATURE COUPLING LAMBDAS FROM 1scn_MD_ENER.edr

10083500 steps (20167 ps) remaining from first run.
Writing statusfile with starting step    1166500 and length   10083500 
steps...
                                 time   2333.000 and length  20167.000 ps

Back Off! I just backed up 1scn_MD_TPR_CONT.tpr to ./#1scn_MD_TPR_CONT.tpr.1#

gcq#162: "Rub It Right Accross Your Eyes" (F. Zappa)


The total time of my simulation is 22ns and as the log file said it runs for 
Step           Time         Lambda
        6109000    12218.00098        0.00000
but  tpbconv use time   2333.000 and length  20167.000 ps for the continue 
file. The output control in my mdp file are the fallowing:
  
  ; Output Control
nstxout             =  500
nstvout             =  500
nstfout             =  0
nstlog              =  500
nstenergy           =  500


What is wrong?  Why do not continue at the last frame described in the log 
file?? 

Best regards 
Anthony