[gmx-developers] CVS implementation of REMD
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 25 08:47:49 CEST 2005
On Tue, 2005-05-24 at 17:04 -0400, Ken Rotondi wrote:
> Hello all,
> I'm having a bear of a time getting started with REMD in the CVS code.
> I have succeeded in compiling the CVS code with mpi support.
> I've made two .tpr files for two adjacent temperatures, named
> topol0.tpr and topol1.tpr as an initial test, using:
> grompp -v -np 2 -f 1.mdp -po 1out.mdp -c md8.gro -p p39a.top -o
> To start mdrun:
> mdrun -v -multi -np 2 -replex 20 -s topol*.tpr -o
> Fatal error: run input file topol0.tpr was made for 2 nodes, while
> mdrun expected it to be for 1 nodes
> mpirun -np2 mdrun -multi -v -np 2 -replex 20 -s topol*.tpr -o
> returns the mpirun man page
> This is a single processor box, but I don't see that effecting the
> number of processes that can be run (just the speed with which they
> will finish).
> What am I doing wrong?
-np 2 flag for grompp should be left out. all mdruns run on one
> How are the input and output files specified in the mdrun command
> (using a * wildcard)?
no, by leaving out the number.
topol.tpr will be translated to topol0.tpr etc.
> Unfortunately the CVS manual does not include the Appendix with the
> manual pages in it, however, mdrun -h should provide the same
> Thanks for any help,
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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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