[gmx-users] Problem with continuation of simulation

[Sridhar Acharya]

Hello,

I had carried out a 20ns protein simulation on Gromacs v3.2.1. Later I 
continued the simulation on Gromacs v3.3.
I ran the following command supplying the energy file and trajectory 
file. But the program gave error and stopped (log message is given below).

Since I read that supply of energy file is not absolutely required. I 
again ran tpbconv without -e option for another 10ns. This time the 
program ran with the warning message that the continuation will not be 
exact.
"WARNING: The simulation uses pressure and/or Nose-Hoover temperature 
coupling,
         the continuation will only be exact when an energy file is 
supplied".

When I plotted the trajectory of the Potential energy, I found the 
difference, with PE much below than the previous simulation (PE dropped 
from -559000 to -561000). Can I use the data of this additional 
simulation, or is it a drastic variation, that I need to take care of?

Thank you,
expecting your suggessions.

######################################################################################
[msridhar at cdfd-grid-node10 TRAJEC_WT]$  tpbconv  -s 
../OTHERS_WT/b4md_1cyp_WT.tpr -f rerereafter15_WT.trr  -e 
../OTHERS_WT/rerereafter15_WT.edr -o new.tpr -until 30000


                       :-)  G  R  O  M  A  C  S  (-:

                  Gromacs Runs On Most of All Computer Systems

                             :-)  VERSION 3.3  (-:


      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 ../OTHERS_WT/b4md_1cyp_WT.tpr  Input        Generic run input: tpr tpb
                                   tpa xml
  -f rerereafter15_WT.trr  Input, Opt!  Full precision trajectory: trr trj
  -e ../OTHERS_WT/rerereafter15_WT.edr  Input, Opt!  Generic energy: edr ene
  -n      index.ndx  Input, Opt.  Index file
  -o        new.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  30000  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 ../OTHERS_WT/b4md_1cyp_WT.tpr
Reading file ../OTHERS_WT/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision)
Note: tpx file_version 24, software version 40
Note: nLincsIter not in run input file, setting it to 1
Modifying ir->bUncStart to TRUE

READING COORDS, VELS AND BOX FROM TRAJECTORY rerereafter15_WT.trr...

trn version: GMX_trn_file (single precision)
Read frame    684: step 341344 time 20000.000

Using frame of step 341344 time 20000
Opened ../OTHERS_WT/rerereafter15_WT.edr as single precision energy file
Reading frame     60 time 19917.312
-------------------------------------------------------
Program tpbconv, VERSION 3.3
Source code file: enxio.c, line: 358

Fatal error:
Could not find energy term named 'Pcoupl-Mu-XX'
-------------------------------------------------------

"Stop Drinking My Beer !" (The Amps)
#########################################################################################

-- 
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
http://www.cdfd.org.in
email: sridhar at cdfd.org.in
Phone: Lab: 08413-235467*2044
Mobile: 9866147193


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