[gmx-users] RE: GROMACS96 proper dihetral parameters/OPLS

[Justin Lemkul]

On 11/22/12 3:20 AM, Junfang.Zhang at csiro.au wrote:
> Hi Justin
>
>
> Thank you very much for your prompt reply!
>
> I have used GROMACS96 force field to simulate pure coal density. It perfectly matches the real coal density.
>
> Now I want to apply this coal model to investigate gas adsorption in coal. But I do not think GROMACS can do this. Therefore, I am thinking of running different software which could allow me to perform grand canonical Monte Carlo simulations to produce isotherm adsorption curve by applying GROMACS96 force field, but the software does not include the proper dihedrals in the similar form as the periodic dihedrals in GROMACS96.
>
> Actually, I am not transferring the GROMACS96 proper dihedral parameters to the OPLS proper dihedral parameters, but intended to implement the  GROMACS96 force field in a different software.
>

All the parameters you need are in the force field subdirectory that you used in 
Gromacs, and all the equations are in the manual.  I can't offer you any 
specific advice on generically implementing some force field into some other 
software, but if it can be done it's all a matter of unit conversion and syntax 
in the required files, I'm sure.

-Justin

>
> Regards and thanks
>
> Junfang
>
>
>
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin Lemkul
> Sent: 2012年11月22日 13:42
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] RE: GROMACS96 proper dihetral parameters/OPLS
>
>
>
> On 11/21/12 9:56 PM, Junfang.Zhang at csiro.au wrote:
>> Dear GROMACS users
>>
>> I am just wondering if you could help with transferring the GROMACS96 proper dihetral parameters to the OPLS proper dihedral parameters or point me to some references.
>>
>
> Gromos96 uses periodic dihedrals and OPLS uses Ryckaert-Bellemans.  The forms of
> these two are very different and it isn't clear to me how the two would be
> interconverted.  If you want to use OPLS and the dihedral isn't defined, derive
> it in a manner consistent with the original force field.  Trying to transfer
> different parameters between force fields probably isn't worth the effort.
>
>> GROMACS96 dihedral:
>>
>>
>> OPLS dihedral:
>>
>>
>> My second question is if CO2 has been parameterised in GROMACS96 force field.
>>
>
> Maybe, but note that no such force field exists.  Your literature searching will
> probably be more fruitful if you use correct terminology (Gromos96), which has a
> number of parameter sets that have been developed over the years.
>
> -Justin
>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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