Sir, <br><br> System is a protein with 123 aa. No modifications were made on the pdb file, <br>and it was submitted to pdb2gmx by removing all HETATMs, retaining only protein <br>atoms. topology was created entirely by pdb2gmx and no other molecule was introduced.<br>
<br> I will go through the OPLSAA paper, but if I increase rlist to 1.4nm without reducing<br>rvdw according to<font style="font-family: arial,helvetica,sans-serif; color: rgb(0, 0, 0);" color="#ffffff" size="2"> "The Origin of Layer Structure</font> Artifacts in Simulations of Liquid Water"<br>
- JCTC, 2006, 2, 1-11, will it not cause orderedwater shell during simultion?<br style="font-family: arial,helvetica,sans-serif;"><br><br>Thanking you<br>M. Kavyashree<br><br><div class="gmail_quote">On Sat, Jan 22, 2011 at 12:27 AM, 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>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Sir,<br>
<br>
What exactly can be wrong with the topology? As I tried with<br>
</blockquote>
<br></div>
I don't know, what's in your system? Was the topology created entirely by pdb2gmx, or have you introduced some other molecules that you've parameterized?<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;">
different PDBs of same structure at higher resolutions too, I am getting<br>
almost similar charge group radii, so can you kindly elaborate about<br>
what can go wrong in the topology to get such values?<br>
<br>
</blockquote>
<br></div>
Large charge groups indicate that a fair number of atoms have been included in the same charge group. Usually only two or three atoms are in a charge group, rendering them fairly small. With PME, the effects may not be that large, i.e. <a href="http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html</a>, but it's still worth investigating what your largest charge group is that's causing this problem. If the topology is sound and is based entirely upon standard force field files, it may suffice to simply increase rlist to 1.4 nm, leaving all the other cutoffs at 1.0, which I believe is standard for OPLS (but don't just take my word for it).<br>
<br>
-Justin<br>
<br><div><div class="h5">
<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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