Yanmei Song wrote:
Hi,Justin:
Thanks for your response.
I have read that part and still confused. Does it mean that if I
choose the ffoplsaa.itp in my top, I used the RB potential for
Dihedrals or the periodic type? Also actually I can only get the
parameters for phi, cp and mult (listed above) Can I use these
parameters directly for my itp user ffoplsaa force field? Thanks a
lot!
OPLS does use the R-B potential. It looks like that topology is a PRODRG
product, in which case, no, your topology is not suitable for use with OPLS.
PRODRG generates Gromos-type topologies.
-Justin
2009/1/28 Justin A. Lemkul <jalem...@vt.edu>:
Yanmei Song wrote:
Hi,
I am using ffoplsaa.itp as my force field to do a simulation using
GROMACS.
I have a question about how to write the parameters in dihedrals in
the itp file.
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
1 2 5 6 1 0.0 3.77 3 0.0 3.77 3 ; dih CAA
CBF OAW CBH
2 5 6 9 1 0.0 3.77 3 0.0 3.77 3 ; dih CBF
OAW CBH OAY
5 6 9 10 1 0.0 3.77 3 0.0 3.77 3 ; dih OAW
CBH OAY CBJ
6 9 10 13 1 0.0 3.77 3 0.0 3.77 3 ; dih CBH
OAY CBJ OBA
9 10 13 14 1 0.0 3.77 3 0.0 3.77 3 ; dih OAY
CBJ OBA CBL
Then if I am choosing ffoplsaa.itp force field, what is the meaning
for c0,c1 and m under the [dihedrals]? Since i know that GROMOS and
OPLS force field have a different format for proper dihedrals. For
OPLS it seems there are four other parameter like v1 v2 v3 v4. Then my
question is how can i define the dihedral parameters in itp file based
on ffoplsaa force field in GROMACS? Thanks a lot!
Refer to the manual, section 4.2.12 "Proper Dihedrals."
-Justin
Yanmei
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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