[gmx-users] problem in extending a simulation run

[manindersingh rajawat]

Dear all,

I want extend a 100ns run to 150 ns. For this I use following commands:

gmx convert-tpr -s md_100ns.tpr -extend 50000 -o md_150ns.tpr

gmx mdrun -v -deffnm md_150ns -c md_150ns.pdb

But mdrun taken it as a new run and began a full 150ns run:
starting mdrun 'Protein in water'
75000000 steps, 150000.0 ps

so i stopped it, and run with checkpoint input as following:

gmx mdrun -v -s md_150ns.tpr -cpi state.cpt -c md_150ns.pdb

Reading checkpoint file state.cpt generated: Fri Mar 24 05:39:47 2017


  Version mismatch,
    current program: VERSION 5.0.6
    checkpoint file: VERSION 5.0.2

  Build time mismatch,
    current program: Mon Jul 27 05:11:28 UTC 2015
    checkpoint file: Fri Oct 24 17:49:05 UTC 2014

  Build user mismatch,
    current program: buildd at lgw01-56 [CMAKE]
    checkpoint file: buildd at roseapple [CMAKE]

  Build host mismatch,
    current program: Linux 3.19.0-23-generic x86_64
    checkpoint file: Linux 3.2.0-61-generic x86_64

Gromacs patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.

Using 1 MPI thread
Using 4 OpenMP threads
Compiled SIMD instructions: SSE2 (Gromacs could use AVX2_256 on this
machine, which is better)

WARNING: This run will generate roughly 19040 Mb of data

starting mdrun 'Protein in water'
75000000 steps, 150000.0 ps (continuing from step 50000000, 100000.0 ps).
step 50000600

It starts well from the checkpoint, but due to little confusion i stopped
it. and ran the following command:

gmx mdrun -v -s md_150ns.tpr -cpi state_prev.cpt -c md_150ns.pdb

It gives the following error

Reading file md_150ns.tpr, VERSION 5.0.6 (single precision)
Changing nstlist from 5 to 40, rlist from 1.2 to 1.223


Reading checkpoint file state_prev.cpt generated: Fri Mar 24 05:36:56 2017


  Version mismatch,
    current program: VERSION 5.0.6
    checkpoint file: VERSION 5.0.2

  Build time mismatch,
    current program: Mon Jul 27 05:11:28 UTC 2015
    checkpoint file: Fri Oct 24 17:49:05 UTC 2014

  Build user mismatch,
    current program: buildd at lgw01-56 [CMAKE]
    checkpoint file: buildd at roseapple [CMAKE]

  Build host mismatch,
    current program: Linux 3.19.0-23-generic x86_64
    checkpoint file: Linux 3.2.0-61-generic x86_64

Gromacs patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.


-------------------------------------------------------
Program gmx, VERSION 5.0.6
Source code file:
/build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c, line:
2204

Fatal error:
Failed to lock: md.log. Already running simulation?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

When i run the previous command, that is

gmx mdrun -v -s md_150ns.tpr -cpi state.cpt -c md_150ns.pdb

It starts giving the same error to this also.

Reading checkpoint file state.cpt generated: Fri Mar 24 05:39:47 2017


  Version mismatch,
    current program: VERSION 5.0.6
    checkpoint file: VERSION 5.0.2

  Build time mismatch,
    current program: Mon Jul 27 05:11:28 UTC 2015
    checkpoint file: Fri Oct 24 17:49:05 UTC 2014

  Build user mismatch,
    current program: buildd at lgw01-56 [CMAKE]
    checkpoint file: buildd at roseapple [CMAKE]

  Build host mismatch,
    current program: Linux 3.19.0-23-generic x86_64
    checkpoint file: Linux 3.2.0-61-generic x86_64

Gromacs patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.


-------------------------------------------------------
Program gmx, VERSION 5.0.6
Source code file:
/build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c, line:
2204

Fatal error:
Failed to lock: md.log. Already running simulation?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Please help me to resolve it.

Thanks
-- 
Maninder Singh
Research Fellow,
LSN-104, Computational Biology and Bioinformatics Unit,
Molecular and Structural Biology Division,
CSIR-Central Drug Research Institute,
Sector-10, Janakipuram Extension,
Sitapur road,
Lucknow
India-226031
M: +919129206276
Email: rajawat.manindersingh at gmail.com