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

[Yanmei Song]

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!

2009/1/28 Justin A. Lemkul <jalemkul at 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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-- 
Yanmei Song
Department of Chemical Engineering
ASU