[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS

[Justin A. Lemkul]

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

-- 
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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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