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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