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

[Yanmei Song]

What makes me so confused is that I used this top for the MD run using
ffoplsaa.itp and the there are no error message. Also I got a good
result compared to experiment. Does it mean that what I did is totally
wrong with using this top in combination with OPLS?

Also if I used the atom type in opls_x with the x is less than 135,
then it should be OPLS UA force field right? if I want to use OPLS,
How can we get the top? Thank you so much for your help!

2009/1/28 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> 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 <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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>>
>>
>>
>
> --
> ========================================
>
> 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