[gmx-users] Replica exchange temp. distribution
gmx3 at hotmail.com
Wed Nov 19 11:19:17 CET 2008
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.
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
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,
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"
>>for temperature distributions . However over a high range of temperature there are more
>>4, values given in the optimal tempearture distribution as obtained as an output from
>>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.
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