I really don't think you can get adequate sampling for IDPs that have 40 residues, using full atomic MD.<div><br></div><div><br><div class="gmail_quote">On Wed, Jun 8, 2011 at 3:25 PM, Michael Daily <span dir="ltr"><<a href="mailto:mdaily.work@gmail.com">mdaily.work@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#ffffff" text="#000000">
Do you have some experimental data to compare to your IDP
simulations, like X-ray scattering or some such? I'd imagine that
IDP simulations with either forcefield would only be qualitatively
accurate given that the forcefields are calibrated, as you say, on
rigid proteins and small molecules.<br>
<br>
On 6/8/11 8:00 AM, Thomas Evangelidis wrote:
<blockquote type="cite">Dear Prof van der Spoel and GROMACS users,<br>
<br>
I have read the article "Scrutinizing Molecular Mechanics Force
Fields..." where it is demonstrated that AMBER99sb yields protein
conformations that are in better agreement with residual dipolar
coupling, J-coupling and NOE data, compared with other force
fields. However, both proteins used for this benchmark study
(ubiquitin and protein G) are rather rigid, so I was wondering if
there is a similar analysis for flexible proteins/peptides. I want
to simulate a few intrinsically disordered proteins/peptides of
length between 40 and 100 aa and would like to know what would be
the best choice of force field to use. Any experience or knowledge
on this matter would be greatly appreciated!<br>
<br>
thanks in advance,<br>
Thomas<br>
<br>
<br>
<br>
<div class="gmail_quote">On 27 May 2011 19:01, David van der Spoel
<span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</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>
<div>On 2011-05-27 17.50, simon sham wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Hi,<br>
I have recently done two simulations on a protein at
high temperature<br>
near its melting temperature. At the beginning I used
CHARMM forcefield,<br>
and then OPLSAA to double check the results. There are
some differences<br>
in the structures between the forcefield used. I know
different<br>
forcefields can give different results. All parameters
in the<br>
simulations were the same except the forcefield. Is
there anyway I can<br>
tell which forcefield gives more reliable results?<br>
<br>
Thanks for the insights,<br>
<br>
Simon<br>
<br>
</blockquote>
</div>
</div>
You might want to check<br>
<br>
Oliver Lange, David van der Spoel and Bert de Groot:
Scrutinizing Molecular Mechanics Force Fields on the
Microsecond Timescale With NMR Data Biophys. J. 99 pp. 647-655
(2010)<br>
<br>
where we compare a number of FFs to NMR data.<br>
<font color="#888888">
<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: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a></font>
<div>
<div><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>
<br clear="all">
<br>
-- <br>
<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou ,
115 27
Athens, Greece<br>
<br>
email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>
</blockquote>
<br>
<br>
<pre cols="72">--
Michael D. Daily, Ph.D.
Postdoctoral Fellow
Qiang Cui group
Department of Chemistry
University of Wisconsin-Madison</pre>
</div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">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<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">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></blockquote></div><br></div>