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, "lam-7.0.6-5.x86_64.rpm,libaio-0.3.103-3.x86_64.rpm,libaio-devel-0.3.103-3.x86_64.rpm and fftw ".
On Thu, Dec 18, 2008 at 1:03 AM, Chitrita Dutta Roy <[email protected]>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. > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD
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