Hi,
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.
Berk
Date: Wed, 19 Nov 2008 10:17:52 +0000
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: Re: [gmx-users] Replica exchange temp. distribution
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
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