[gmx-users] Replica exchange temp. distribution

[Berk Hess]

Hi,

You can run as many replica's you want on one machine.
One "gromacs node" does not have to correspond to a physical
node or core.
If you have 4 nodes, you can use for instance mpirun -np 12
to have 3 replica's per physical node.
Usually this will just work, in some cases you might need to
modify the setup of your MPI environment.

Berk

Date: Wed, 19 Nov 2008 10:17:52 +0000
From: sarbani_c84 at rediffmail.com
To: gmx-users at gromacs.org
Subject: Re: Re: [gmx-users] Replica exchange temp. distribution


  Hi,

     I do understand that reducing the number of replicas will limit my temperature space, 

but gromacs 3.3.2 can run 1 replica per node. Thus having 4 nodes , I can have only 4 

replicas. Thus in case I want to span a temperature space of 313K to 333K using only 4 

replicas, is there any possible method by which I can choose 4 optimal temperature values, 

maintaining a decent exchange-probability value?  



Thanks in advance,

 Sarbani





On Wed, 19 Nov 2008 Mark Abraham wrote :

>sarbani chattopadhyay wrote:

>>  Hi everyone,

>>                   I will like to do Replica exchange simulation on a peptide. We have a single

>>machine with 4 cpus and the gromacs3.3.2 is installed.

>>Thus I will be able to select only 4 temperature values. I came across the  "T-REMD" 

caculator

>>for temperature distributions . However over a high range of temperature there are more 

than

>>4, values given in the optimal tempearture distribution as obtained as an output from 

the "T-

>>REMD" calculator. How to choose the best possible 4 temperature values.

>

>Using explicit solvent with a low number of replicas will severely limit the temperature 

space you can span while achieving exchanges in accessible simulation times. See http://

dx.doi.org/10.1021/ct800016r and references therein.

>

>Mark

>_______________________________________________

>gmx-users mailing list    gmx-users at gromacs.org

>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 

gmx-users-request at gromacs.org.

>Can't post? Read http://www.gromacs.org/mailing_lists/users.php







_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081119/39d91926/attachment.html>