[gmx-users] Gromacs 4 with mpi interface

Venkat Reddy venkat4bt at gmail.com
Thu Dec 18 06:10:30 CET 2008

U just have to modify the .top file, Just add the line "Na+     2" at the
bottom of the file where u can find "SOL       <some number>"and also u have
to substract 2 from the SOL number. Thats it.
Regarding MPI, if u r using MULTIPLE MACHINES....then MPI is useful....
otherwise , if u r using single machine with multiple processors,run the
command "mdrun -np <no.of processors> -s topol -v  -N <no.of processors>"
That's it.Regarding the installation of MPI, first u should install the all
library files that are mentioned in the Gromacs web site,
and fftw ".

On Thu, Dec 18, 2008 at 1:03 AM, Chitrita Dutta Roy
<chitrita.md at gmail.com>wrote:

> Can anyone give me a detailed notes on how to install gromacs 4 with mpi
> feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new
> to using gromacs plz give me as detailed note as possible..
> And after adding some ions using genion when i try to run grompp again
> before final mdrun i get some error telling mismatches in .top and .gro file
> in some atoms although i have changed the top files as normally we should
> adding the ions and changing the total number of solvents accordingly..Why
> is it happening Can anybody help..plzz??
> Thanks.
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Venkat Reddy Chirasani
M.Tech Bioinformatics
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