[gmx-developers] H-REMD restart

[Mark Abraham]

On 01/24/11, Mark Abraham  <mark.abraham at anu.edu.au> wrote:
> 
> 
> 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.
> 

Also, stderr and stdout can have useful diagnostic information here.

Mark


> 
> 
> 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
> > 
> > -- 
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-developers-request at gromacs.org.
> > 
> > 
> 
> 
> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20110124/99774443/attachment.html>