[gmx-users] Re: REMD tutorial

[Mark Abraham]

On 10/02/2012 1:20 PM, bharat gupta wrote:
> Hi,
>
> I am planning to carry out a REMD study on a 12 residue beta-hairpin 
> peptide. I have read the gromacs tutorial for that . I have certain 
> doubts regarding the tutorial :-
>
> 1. Step. 4 says that "run short simulations to have an estimate of the 
> exchange rate (can get a good estimate within ~100 ps) and modify the 
> temperatures if it does not correspond to the wished exchange." Do I 
> have to run short MD of 100 ps for each replica . I am not able to 
> understand this step ??

You want to obtain an real estimate of the exchange acceptance frequency 
before you commit large resources. So do a short REMD simulation to see 
what that frequency is.

>
> 2. I have currently 24 processors available for REMD. The temperature 
> range that I have obtained from tgenerator server has 69 different 
> values (300K-600K). I want to know  how to calculate the no. of 
> processors required for carrying out REMD for a certain temperature 
> range ??

Your system size, number of replicas, temperature range and exchange 
acceptance frequency are interlinked. You can only choose three of them 
independently.

Mark
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