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Hi,<br><br>You can run as many replica's you want on one machine.<br>One "gromacs node" does not have to correspond to a physical<br>node or core.<br>If you have 4 nodes, you can use for instance mpirun -np 12<br>to have 3 replica's per physical node.<br>Usually this will just work, in some cases you might need to<br>modify the setup of your MPI environment.<br><br>Berk<br><br><hr id="stopSpelling">Date: Wed, 19 Nov 2008 10:17:52 +0000<br>From: sarbani_c84@rediffmail.com<br>To: gmx-users@gromacs.org<br>Subject: Re: Re: [gmx-users] Replica exchange temp. distribution<br><br>
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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