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@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 [EMAIL PROTECTED] >Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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