[gmx-users] Re: REMD tutorial

bharat gupta bharat.85.monu at gmail.com
Fri Feb 10 03:20:08 CET 2012


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 ??

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 ??

Kindly clarify these doubts ....


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