sa wrote:
Sorry I forget to say in my previous mail that the values obtained by
g_sigeps_mpi are not similar to the values given in
the GROMOS53A6 ffnonbonded.itp for the OM atom.
I understand that. Everything I said an hour ago
(http://lists.gromacs.org/pipermail/gmx-users/2011-March/059742.html) still
stands. There is some discrepancy that is unclear. The authors of the paper
you cite should be able to explain the disconnect. Converting OM to
sigma/epsilon does not yield the same values given in that paper, so I would
expect that the "backwards" transition would not work, either.
-Justin
OM 8 0.000 0.000 A 0.0022619536 7.4149321e-07
So your advices are welcome.
SA
2011/3/28 sa <[email protected] <mailto:[email protected]>>
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 <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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