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.
If you need an R-B dihedral, you may have to parameterize it yourself; not an
easy task.
-Justin
Yanmei Song wrote:
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!
On Fri, May 15, 2009 at 4:00 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Yanmei Song wrote:
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?
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?
-Justin
On Fri, May 15, 2009 at 3:34 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Please keep all Gromacs-related correspondence on the gmx-users
list. That way, the discussion is archived for the later
benefit of
others, and you have a chance to reach a wider audience of
individuals who may be able to help you.
That said, read the manual, section 4.2.12.
-Justin
Yanmei Song wrote:
Dear Justin:
If I have the parameters of GROMOS force field for the proper
dihedral, which i think they are phi and k for function 1 for
periodic type. I wanted to use OPLS force field. As far as I
know in OPLS the dihedral was RB potential in fuction 3.
So my
question is do you know any method I can transfer this
parameter
to RB parameters? Or these two potentials have no
connections?
Thanks
-- Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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