I went through few papers related to OPLS-AA, but could not find <br>any specific values mentioned for vdw and coulomb intecations..<br>In one of the papers <br>".....In most cases, the intermolecular nonbonded interactions were <br>
truncated at 11Å based on roughly the center-of-mass separations<br>with quadratic smoothing of the interaction energy to zero over the <br>last 0.5 Å. The cutoff for alkenes and acetals was 13 Å, while for<br>propanol, cyclohexane, 2-methyl-2-propanol, phenol, ethyl methyl <br>
sulfide, NMA, DMA, and NMP it was extended to 15 Å....." <br>J. Am. Chem. Soc. 1996, 118, 11225-11236.<br><br><br>So does this cut off refer to coulombic interactions?<br>is it correct if iI use the following parameters for OPLS-AA force field?<br>
<br>-----------------------------------------------------------------------------<br>;NEIGHBOUR SEARCHING<br>nstlist = 10 ; FREQUENCY WITH WHICH NEIGHBOURLIST IS UPDATED<br>ns_type = grid ; TYPE OF NEIGHBOUR SEARCH GRID OR SIMPLE<br>
pbc = xyz ; DIRECTION OF PERIODIC BOUNDARY CONDITIONS USAGE<br>rlist = 1.4 ; CUT-OFF DISTANCE FOR SHORT RANGE NEIGHBOUR LIST<br><br>;ELECTROSTATICS<br>coulombtype = PME ; METHOD FOR CALCULATING COULOMIC INTERCATION - PARTICLE MESH EWALD<br>
rcoulomb = 1.4 ; CUTOFF DISTANCE FOR ELECTROSTATIC INTERACTIONS<br>epsilon_r = 1 ; RELATIVE DIELECTRIC CONSTANT<br><br>;VAN DER WAALS<br>vdwtype = Switch ; METHOD FOR TREATING VANDERWAAL'S FORCES<br>
rvdw_switch = 0.9<br>rvdw = 1.00 ; CUTOFF DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS<br>--------------------------------------------------------------------------------------------------------------------<br>
<br><br>Thanks<br>MKS<br><br><br><div class="gmail_quote">On Sat, Jan 22, 2011 at 6:41 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>
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>
</blockquote>
<br></div>
As I said before, read the OPLS paper. 1.35 nm does not sound right.<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;">
Thank you<br>
M. Kavyashree<div class="im"><br>
<br>
On Sat, Jan 22, 2011 at 6:26 PM, 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>
System is a protein with 123 aa. No modifications were made<br>
on the pdb file,<br>
and it was submitted to pdb2gmx by removing all HETATMs,<br>
retaining only protein<br>
atoms. topology was created entirely by pdb2gmx and no other<br>
molecule was introduced.<br>
<br>
I will go through the OPLSAA paper, but if I increase rlist<br>
to 1.4nm without reducing<br>
rvdw according to "The Origin of Layer Structure Artifacts in<br>
Simulations of Liquid Water"<br>
- JCTC, 2006, 2, 1-11, will it not cause orderedwater shell<br>
during simultion?<br>
<br>
<br>
You're using PME. In the first paragraph of the introduction, it is<br>
stated that the spurious effect does not occur with PME.<br>
<br>
-Justin<br>
<br>
<br>
Thanking you<br>
M. Kavyashree<br>
<br>
<br>
On Sat, Jan 22, 2011 at 12:27 AM, Justin A. Lemkul<br>
<<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>><br></div><div><div></div><div class="h5">
<mailto:<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<br>
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<br>
too, I am<br>
getting<br>
almost similar charge group radii, so can you kindly<br>
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<br>
been<br>
included in the same charge group. Usually only two or three<br>
atoms<br>
are in a charge group, rendering them fairly small. With<br>
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<br>
group is<br>
that's causing this problem. If the topology is sound and is<br>
based<br>
entirely upon standard force field files, it may suffice to<br>
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>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
<br>
231-9080<br>
<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>
<mailto:<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> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><div><div></div><div class="h5">
<br>
<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<br>
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>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br>
<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>
<br>
-- ========================================<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> <<a href="http://vt.edu" target="_blank">http://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>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<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<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>
<mailto:<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>
<br>
<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <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>
========================================<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>