[gmx-users] REMD and mpi

[David van der Spoel]

pascal.baillod at epfl.ch wrote:
> Dear community,
> 
> I am currently testing the gromacs-3.3 implementation of REMD and have the
> following questions..
> 
> 1) Is it possible to write the different REMD trajectories on different
> locations? I would be interested in writing the trajectories locally, that is,
> on the disk next to the compute node, on a machine that dose not have fast
> switches. If that is not possible, is there any benchmark on the bottleneck
> created by many compute nodes writing REMD data on a same disk, on a machine
> that dose not have fast switches (max 1gbps)?
You can e.g. write mdrun -o /tmp/traj.trr where /tmp is the local disk.

> 
> 2) I have tried running NPT-REMD with 3 replicas, at 300, 305 and 310 K. The
> barostat of my 3 .mdp input files has rep_p = 1.0. I get the following error
> message:
> Fatal error:
> The reference pressure decreases with increasing temperature
The pressures must be equal, I suspect that you have not set the same 
pressure coupling info in all mdp files
> 
> If I do the same test with the first 2 replicas only (300 and 305K), I do not
> get this error message and things seem to run fine. 
> 
> 3) Is there any script to get statistics of swaps? In order to compute the
> temperature series visited by a replica, for example..
> 
> Thank you very much for your help!
> 
> Pascal
> 
> 
> 
> 
> 
> *******************************************************************************
> Pascal Baillod (PhD student) 
> *******************************************************************************
> Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
> Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
> Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
> Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
> CH-1015 Lausanne	
> *******************************************************************************
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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