[gmx-users] query regarding replica exchange

[Joshua L. Phillips]

You will need a file formatted like the following:

node0 slots=4 max_slots=4
node1 slots=4 max_slots=4
...
node9 slots=4 max_slots=4

You will then need to use the -hostfile option to supply the filename to
either mpiexec or mpirun (not mdrun).

-- Josh

On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote:
> Hi,
> 
> 
>   I am planning to run replica exchange simulation using gromacs
> 4.0.7 . I have read the manual about REMD. Only thing I wanted to know
> is that how I can specify the name of host-machines where I am
> planning to run the simulations. 
> 
> 
> I have 10 different quad-core computers each intra-connected with the
> other each running OPENMPI. I want to run 20 replica each using 2
> cores in parallel.
> 
> 
> So, I was wondering whether I have to create any file containing the
> names of those machines . If so, can someone give an example of format
> of the file which contain those names ? Finally, what keyword I should
> use in mdrun to specify that file for running replica exchange. 
> 
> 
> Also, I am not using any PBS for submitting jobs.
> 
> 
> Sanku
> 
> 
> 
> 
> 
> 
>  
> 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
Joshua L. Phillips
Ph.D. Candidate - School of Engineering
University of California, Merced
jphillips7 at ucmerced.edu