Yes, I understand that. But then this is a protein in water simulation with CHarmm forcefield and I cannot find a reason as to why does this happen(esp after variable number of steps)? I have checked the .pdb files generated for the steps where Lincs fails and it seems that H atoms for atleast 1 sidechain are in incorrect positions(usually clashing). There doesn't seem to be a good way of analyzing this error. If you have any suggestions I would be eager to try them.<br>
<br>Pooja<br><br><div class="gmail_quote">On Sat, Oct 30, 2010 at 3:40 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
For Replica exchange, is there any advantage of in using SHAKE over LINCS(other than the stepsize)?<br>
I am running an REM simulation and the simulation stops after running for variable number of steps (100000, 10000000 etc.) because some bond moves more than 30 degrees and LINCS gives a warning.<br>
<br>
</blockquote>
<br></div>
It has been said (check the archive) that LINCS is more stable. Just because you're getting LINCS warnings does not mean the constraint algorithm is to blame, it's just the first algorithm that fails when your model physics implodes.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Pooja<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>