[gmx-users] Problem with continuation of files using checkpoint files

[Monika Sharma]

Dear All,
I am doing protein simulations using Gromacs4.0.2. For continuation or
extension of runs, i am using tpbconv command. In the manual its given that
for exact binary identical run, one needs to use checkpoint file with mdrun.
So, for the tpbconv generated file when I am using checkpoint. I am getting
warnings as below. Gromacs is  parallelly installed, but I am using on
single node.
> tpbconv_4 -s md_1.tpr -f md_1.trr -e md_1 .edr -o md_2.tpr -extend 2000.0
> mdrun_4 -s md_2.tpr -cpi md_1.cpt -deffnm md_2.tpr &

I am getting the message as:

Reading checkpoint file md_1.cpt generated: Thu Feb 12 08:42:50 2009

Gromacs binary or parallel settings not identical to previous run.
Continuation still works, but is not guaranteed to be binary identical,
 see the log file for details.

Gromacs binary or parallel settings not identical to previous run.
Continuation still works, but is not guaranteed to be binary identical.


Looking at the log file:

Reading checkpoint file md_1.cpt
  file generated by:     mdrun_4
  file generated at:     Thu Feb 12 08:42:50 2009
  GROMACS build time:    Wed Dec 24 23:09:37 EST 2008
  GROMACS build user:    compute at localhost.localdomain
  GROMACS build machine: Linux 2.6.9-67.ELsmp x86_64
  simulation part #:     1
  step:                  500000
  time:                  2000.000000

  #PP-nodes mismatch,
    current program: 2
    checkpoint file: 1

If anyone can please suggest, what might be the problem. What is meant by PP
nodes mismatch?
Thanks in advance.

Regards
Monika
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