[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

[sa]

>
> 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

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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
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