Dear Justin:<br><br>Thanks for your response. I saw this in the ffoplsaabon.itp, which I think is a Periodic potential.<br><br> [ dihedraltypes ]<br>; i j k l func coefficients<br>; Added DvdS for Quartz simulations<br>
SI OS 1 0.000 3.766 3<br>
SI OH 1 0.000 3.766 3<br><br>Does this mean that we can still use a periodic potential combined with OPLS force field since it seems OPLS also consists of the periodic potential besides RB. It doesn't have to be necessary to use RB for the proper dihedral when you use OPLS force field, right? <br>
<br>Thank you so much for your help!<br><br><br><div class="gmail_quote">On Fri, May 15, 2009 at 6:37 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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;"><br>
There is a periodic dihedral within ffoplsaabon.itp which points to a reference. Perhaps these are the parameters you are referring to. If not, check out the bottom of ffoplsaabon.itp and read that paper to see if the parameters will suit your needs.<br>
<br>
If you need an R-B dihedral, you may have to parameterize it yourself; not an easy task.<br>
<br>
-Justin<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;"><div>
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><div>
On Fri, May 15, 2009 at 4:00 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>
Yanmei Song wrote:<br>
<br>
Yes, I have read that part and still have no idea how can I do<br>
that. That part tells us how to transfer from the OPLS<br>
parameters Vi to RB potential in GROMOS force field Ci. Now<br>
what I have is phi and k for periodic potential. Is there any<br>
way I can get Ci for RB potential from phi and k in order to use<br>
OPLS force field?<br>
<br>
<br>
I don't know if there is a direct conversion. There are, however,<br>
over 1000 existing dihedrals in ffoplsaabon.itp; which dihedral are<br>
you looking for that you can't find?<br>
<br>
-Justin<br>
<br>
On Fri, May 15, 2009 at 3:34 PM, 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>
<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>
Please keep all Gromacs-related correspondence on the gmx-users<br>
list. That way, the discussion is archived for the later<br>
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.<br>
So my<br>
question is do you know any method I can transfer this<br>
parameter<br>
to RB parameters? Or these two potentials have no<br>
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>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div><div>
</div><div><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>
<br>
<br>
<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>
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>
<br>
<br>
<br>
<br>
-- <br>
Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
</div></div></blockquote><div><div></div><div>
<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>
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</blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>