They are CH3-SI-O-SI, SI-O-SI-CH3 and SI-O-SI-O. I have looked up ffoplsaabon.itp. it doesn't include any dihedral consisting of SI. And the literatures only have the parameters for periodic potential. Thank you so much for your kind help!<br>
<br><div class="gmail_quote">On Fri, May 15, 2009 at 4:00 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Yanmei Song wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Yes, I have read that part and still have no idea how can I do that. That part tells us how to transfer from the OPLS parameters Vi to RB potential in GROMOS force field Ci. Now what I have is phi and k for periodic potential. Is there any way I can get Ci for RB potential from phi and k in order to use OPLS force field?<br>
<br>
</blockquote>
<br></div>
I don't know if there is a direct conversion. There are, however, over 1000 existing dihedrals in ffoplsaabon.itp; which dihedral are you looking for that you can't find?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
On Fri, May 15, 2009 at 3:34 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>
Please keep all Gromacs-related correspondence on the gmx-users<br>
list. That way, the discussion is archived for the later benefit of<br>
others, and you have a chance to reach a wider audience of<br>
individuals who may be able to help you.<br>
<br>
That said, read the manual, section 4.2.12.<br>
<br>
-Justin<br>
<br>
<br>
Yanmei Song wrote:<br>
<br>
Dear Justin:<br>
<br>
If I have the parameters of GROMOS force field for the proper<br>
dihedral, which i think they are phi and k for function 1 for<br>
periodic type. I wanted to use OPLS force field. As far as I<br>
know in OPLS the dihedral was RB potential in fuction 3. So my<br>
question is do you know any method I can transfer this parameter<br>
to RB parameters? Or these two potentials have no connections?<br>
Thanks<br>
<br>
-- Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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>
<br>
<br>
<br>
<br>
-- <br>
Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>