[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS
Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 29 04:05:05 CET 2009
Yanmei Song wrote:
> 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
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.
> 2009/1/28 Justin A. Lemkul <jalemkul at vt.edu>:
>> Yanmei Song wrote:
>>> I am using ffoplsaa.itp as my force field to do a simulation using
>>> 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 A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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