[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS
Yanmei Song
ysong30 at asu.edu
Thu Jan 29 05:34:34 CET 2009
[ 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
Sorry to bother you so much times. Above is the real parameter I used
in my top file which probably specified the dihedrals as periodic
(function 1) . But I also used OPLS force field which should read
different parameters as RB. So when the MD runs, does it just read
this parameters in the periodic dihedrals as a RB parameter? If my top
is in a wrong form, how can md runs well and give a good result?
2009/1/28 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> 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
>>>>>
>>>>> ========================================
>>>>> _______________________________________________
>>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>>>
>>> ========================================
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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--
Yanmei Song
Department of Chemical Engineering
ASU
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