Hi,<div><br></div><div>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 :-</div><div><br></div><div>1. Step. 4 says that "<span style="background-color:rgb(255,255,255);color:rgb(79,107,114);font-family:arial,verdana,helvetica;font-size:12px;line-height:18px">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.</span>" Do I have to run short MD of 100 ps for each replica . I am not able to understand this step ??</div>
<div><br></div><div>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 ??</div>
<div><div><br></div><div>Kindly clarify these doubts ....</div><div><br></div><div>Regards<br clear="all"><div><br></div>-- <br>Bharat<br><br>
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