Thanks for the reply. Since I need to study the effect of beta-hairpin turn design on protein folding . I thought that first unfolding and then refolding would give the change in folding time. As you told that to do such a task would require large computational power. Is there any other method in MDS that could be used ??<br>
<br><div class="gmail_quote">On Wed, Jan 4, 2012 at 10:52 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 4/01/2012 12:35 PM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks for all your replies. I want to know this can be done in gromacs or not - using REMD with structure based models generated from SMOG server to study protein folding and unfolding ??.<br>
</blockquote>
<br></div>
Well, it can be done, but you probably don't have enough computer to fold a 230 residue protein at atomistic resolution (or maybe even coarse-grained).<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Also, I have a question about how to determine the exchange probablities for a particular REMD experiment and also how many replicas do we need to consider, does that depend on the temperature list generated from the T_REMD server??<br>
</blockquote>
<br></div>
There's a significant literature on these subjects. I suggest you read some of it. Short answer: pick the highest temperature according to the size of the largest barrier you expect to cross (good luck guessing that), have around 20% exchange acceptance, and be prepared to observe where the replica-flow bottle necks are and to iteratively refine you temperatures.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="HOEnZb"><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
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