[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 28 13:27:11 CEST 2011
sa wrote:
> Thank you Justin for your response
>
>
> I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137
> and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol
> 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and
> C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used
> the following command
>
I cannot explain this discrepancy. Going back to the actual 53A6 source
(Oostenbrink et al. JCC 2004: 25: 1656-1676), the parameters in ffnonbonded.itp
are correct with respect to the original force field. The fact that Poger et
al. claim the parameters are the same does not make sense to me. You may wish
to contact the authors of that paper directly if you have questions about
reproducing their results. I also find it curious that they list their values
in sigma/epsilon rather than the conventional C6/C12 used by Gromos96 force fields.
-Justin
> g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output
>
> c6 = 4.66239e-03, c12 = 4.44320e-06
> sigma = 0.31370, epsilon = 1.22310
> Van der Waals minimum at 0.352116, V = -1.2231
>
> Fit of Lennard Jones (12-6) to Buckingham:
> A = 199065, B = 34.0796, C = 0.00466239
>
> Back Off! I just backed up potje.xvg to ./#potje.xvg.8#
>
> gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen)
>
>
> Did I miss something ?
>
> Thank you again for your help
>
> SA
>
>
>
>
> sa wrote:
> > Dear All,
> >
> > I would like to compute the C6 and C12 LJ terms for the GROMOS
> 53A6 ff
> > for a new atom type and incorporate them in my ffnonbonded.itp. Does
> > anybody know the mathematical expressions used to obtain these terms
> > from a sigma (nm) and an epsilon (kj/mol) values manually.
> >
>
> g_sigeps can do this for you. Otherwise, you can convert between
> the two common
> forms of the Lennard-Jones equation.
>
> -Justin
>
> > Thank you for your help.
> >
> > SA
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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