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 ?? 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 .... Regards -- Bharat
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