On 11/22/12 3:20 AM, junfang.zh...@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-boun...@gromacs.org [mailto:gmx-users-boun...@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.zh...@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
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