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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