[gmx-developers] H-REMD restart

[Mark Abraham]

On 01/24/11, Luca Bellucci  <luca.bellucci_s3 at unimore.it> wrote:
> hanks Mark for quick replay.
> it is 4.5.3
> This is the log file at restart point.
> 
> -----------------------------------------------------------
> Restarting from checkpoint, appending to previous log file.
> 
> Log file opened on Sun Jan 23 23:40:07 2011
> Host: ionode8  pid: 2916  nodeid: 0  nnodes:  64
> The Gromacs distribution was built Thu Nov 18 14:35:49 CET 2010 by
> cin0644a at loginfn (Linux 2.6.16.60-0.42.10-ppc64 ppc64)
> [..]
> Initializing Replica Exchange
> Repl  There are 64 replicas:
> Multi-checking the number of atoms ... OK
> Multi-checking the integrator ... OK
> Multi-checking init_step+nsteps ... OK
> Multi-checking first exchange step: init_step/-replex ... OK
> Multi-checking the temperature coupling ... OK
> Multi-checking the number of temperature coupling groups ... OK
> Multi-checking the pressure coupling ... OK
> Multi-checking free energy ... OK
> [..]
> 

Seeing the whole logfile up to the first energy output would be more helpful.

Mark


> 
> Started mdrun on node 0 Sun Jan 23 23:40:07 2011
> 
> 
> > On 24/01/2011 8:57 AM, Luca Bellucci wrote:
> > > Dear all,
> > > I known that in repl_ex.c is implemented the
> > > H-REMD.  It seems to work, however
> > > H-REMD is not documented, thus I am testing it.
> > > I performed a test  in a BlueGene cluster:
> > >
> > > mpirun -mode VN -np 4096 mdrun_mpi_bg  -s md.tpr -np 16 -multi 128
> > > -replex 2000
> > >
> > > it works fine.
> > >
> > > I restarted with this command:
> > >
> > > mpirun -mode VN -np 4096 mdrun_mpi_bg   -s md.tpr -cpi state.cpt -append
> > > -np 16 -multi 128 -replex 2000
> > >
> > > I followed the GROMACS  "Doing Restarts" section, however it does not
> > > work as expected; the trajecory and energy files are reinitialized and I
> > > lost most of the MD informations.
> > > Only log files were updated as expected.
> >
> > Is this with the latest GROMACS version? If not, please try that.
> >
> > Mark
> 
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