<P>
Hi,<BR>
I do understand that reducing the number of replicas will limit my temperature space, <BR>
but gromacs 3.3.2 can run 1 replica per node. Thus having 4 nodes , I can have only 4 <BR>
replicas. Thus in case I want to span a temperature space of 313K to 333K using only 4 <BR>
replicas, is there any possible method by which I can choose 4 optimal temperature values, <BR>
maintaining a decent exchange-probability value? <BR>
<BR>
Thanks in advance,<BR>
Sarbani<BR>
<BR>
<BR>
On Wed, 19 Nov 2008 Mark Abraham wrote :<BR>
>sarbani chattopadhyay wrote:<BR>
>> Hi everyone,<BR>
>> I will like to do Replica exchange simulation on a peptide. We have a single<BR>
>>machine with 4 cpus and the gromacs3.3.2 is installed.<BR>
>>Thus I will be able to select only 4 temperature values. I came across the "T-REMD" <BR>
caculator<BR>
>>for temperature distributions . However over a high range of temperature there are more <BR>
than<BR>
>>4, values given in the optimal tempearture distribution as obtained as an output from <BR>
the "T-<BR>
>>REMD" calculator. How to choose the best possible 4 temperature values.<BR>
><BR>
>Using explicit solvent with a low number of replicas will severely limit the temperature <BR>
space you can span while achieving exchanges in accessible simulation times. See http://<BR>
dx.doi.org/10.1021/ct800016r and references therein.<BR>
><BR>
>Mark<BR>
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