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. 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
