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

[Justin A. Lemkul]

Yanmei Song wrote:
> 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?
> 

Well, the numbers in the .top for the dihedrals were designed to be components 
of a periodic dihedral (function type 1 in the .top), which is not of the same 
form as an R-B dihedral (function type 3).  My guess would be that the 
parameters you have specified are not appropriate for use 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!
> 

I suppose you would have OPLS UA, as far as your atom types are concerned.  I 
don't know for sure, I've never used the UA version of OPLS.  If you want the 
.top for your own molecule, you may have to write it by hand, perhaps even using 
the PRODRG topology as a skeleton (along with a thorough understanding of 
Chapter 5 of the manual, as Mark advised).  Depending on the size of your 
molecule, this manual process may be a chore, so you could also consider making 
an  entry for your molecule within ffoplsaa.rtp.  Make a local copy in the 
working directory to ensure that you don't break something by accident!

-Justin

> 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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> 
> 
> 

-- 
========================================

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

========================================