[gmx-users] Gromacs 4 with mpi interface

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 18 07:11:06 CET 2008


Please don't "top post", particularly when responding to multiple topics 
in one email, as it makes it hard for people to understand the context 
of your remarks. A better approach is to insert new paragraphs after the 
text you refer to. You can also appear to be a more credible source of 
good advice by spelling "you" and "are" correctly, and avoiding ALL 
CAPITALS. Abbreviations are good for casual or bandwidth-limited 
situations, which don't really apply here. :-)

Here's a good link on how to ask and answer questions well :-) 

> 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>"

MPI is needed for any form of parallelism with GROMACS.

> 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 ".

Rather than copying and pasting information, a link like 
http://www.gromacs.org/content/view/23/33/ is usually more appropriate.


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