[gmx-users] Re: REMD tutorial
Mark.Abraham at anu.edu.au
Fri Feb 10 08:20:38 CET 2012
On 10/02/2012 1:20 PM, bharat gupta wrote:
> 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
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