[gmx-users] Replica exchange temp. distribution

[sarbani chattopadhyay]

  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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081119/608b11c2/attachment.html>