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On 10/02/2012 1:20 PM, bharat gupta wrote:
<blockquote
cite="mid:CAAh+zSX2zmYRefgF-0qRw_ckTa8ufJkiP_t=1bxgjXtTWSqH+g@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAAh+zSX2zmYRefgF-0qRw_ckTa8ufJkiP_t=1bxgjXtTWSqH+g@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
Your system size, number of replicas, temperature range and exchange
acceptance frequency are interlinked. You can only choose three of
them independently.<br>
<br>
Mark<br>
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