<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<title></title>
</head>
<body text="#000000" bgcolor="#ffffff">
On 4/21/2011 11:37 PM, Juliette N. wrote:
<blockquote
cite="mid:BANLkTimKspAaJpgi941V9OHVJ2fJum9gZA@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">
<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">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
I have a quick enquiry whether temperature affects
pontetial energy<br>
terms. Does T is accounted for to parametrize OPLS FF? Do
bonded and<br>
nonboded energies vary with T?<br>
<br>
</blockquote>
</div>
Have you tried?<br>
Try to read up on heat capacity.<br>
<br>
</blockquote>
<div>Hi David,<br>
<br>
Yes it affects potential. My question is whether this
dependence is accounted for in parametrization (k constants in
harmonic potentials..)</div>
</div>
</blockquote>
<br>
The generated parameters have no explicit T-dependence, so the
functions in which they appear do not have T-dependence either.<br>
<br>
If you want to know how a force field was parametrized, then there's
no substitute for getting the literature and reading it.<br>
<br>
<blockquote
cite="mid:BANLkTimKspAaJpgi941V9OHVJ2fJum9gZA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> or it affects say nb interactions in the sense that at
higher T particles move around faster and it might be that LJ
does not attract molecules as it would at lower T. <br>
</div>
</div>
</blockquote>
<br>
AFAIK, the physical interactions modelled by the LJ potential are
not dependent on particle velocities, so why should the LJ "not
attract molecules" at higher T? Something moving faster doesn't mean
it's less attracted to things that it would be attracted to when
traveling slower... gravity doesn't magically suspend for an
aeroplane...<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimKspAaJpgi941V9OHVJ2fJum9gZA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
Thanks,<br>
Jennifer N.<br>
<br>
</blockquote>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a moz-do-not-send="true" href="mailto:spoel@xray.bmc.uu.se"
target="_blank">spoel@xray.bmc.uu.se</a> <a
moz-do-not-send="true" href="http://folding.bmc.uu.se"
target="_blank">http://folding.bmc.uu.se</a><br>
<font color="#888888">
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Thanks,<br>
Jennifer N.<br>
<br>
</blockquote>
<br>
</body>
</html>