Sir, <br><br> Yes sir I am using PME. And one more thing I noticed was, the protein has<br>7 disulphide bonds, so when I reduce all the cystine to cysteine or to alanine,<br>the the sum of charge group radii reduces from 0.31..nm to 0.30..nm and also the <br>
value of this is identical in case of alanine mutation or cysteine mutation.<br> I finalised on the value of rlist = rcolomb = 1.35nm so as not to take risk. <br>is that fine?<br> <br>Thank you <br>M. Kavyashree<br>
<br><div class="gmail_quote">On Sat, Jan 22, 2011 at 6:26 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>
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>
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 "The Origin of Layer Structure Artifacts in Simulations of Liquid Water"<br>
- JCTC, 2006, 2, 1-11, will it not cause orderedwater shell during simultion?<br>
<br>
</blockquote>
<br></div>
You're using PME. In the first paragraph of the introduction, it is stated that the spurious effect does not occur with PME.<br>
<br>
-Justin<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>
Thanking you<br>
M. Kavyashree<div><div></div><div class="h5"><br>
<br>
On Sat, Jan 22, 2011 at 12:27 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Kavyashree M wrote:<br>
<br>
Sir,<br>
<br>
What exactly can be wrong with the topology? As I tried with<br>
<br>
<br>
I don't know, what's in your system? Was the topology created<br>
entirely by pdb2gmx, or have you introduced some other molecules<br>
that you've parameterized?<br>
<br>
<br>
different PDBs of same structure at higher resolutions too, I am<br>
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>
<br>
Large charge groups indicate that a fair number of atoms have been<br>
included in the same charge group. Usually only two or three atoms<br>
are in a charge group, rendering them fairly small. With PME, the<br>
effects may not be that large, i.e.<br>
<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>,<br>
but it's still worth investigating what your largest charge group is<br>
that's causing this problem. If the topology is sound and is based<br>
entirely upon standard force field files, it may suffice to simply<br>
increase rlist to 1.4 nm, leaving all the other cutoffs at 1.0,<br>
which I believe is standard for OPLS (but don't just take my word<br>
for it).<br>
<br>
-Justin<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
========================================<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
</div></blockquote>
<br>
-- <br>
========================================<div><div></div><div class="h5"><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>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>