[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family
sagmx.mail at gmail.com
Mon Mar 28 13:00:09 CEST 2011
> 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
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 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
> forms of the Lennard-Jones equation.
> > 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
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