On 2011-03-28 14.07, 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.
OM 8 0.000 0.000 A 0.0022619536 7.4149321e-07
Difficult to compare this way.
note that gromos does not use simple combination rules.
For OM there are different C12 (IIRC) depending on the interacting atom.
You should look only at the
[ nonbond_types]
section
So your advices are welcome.
SA
2011/3/28 sa <sagmx.m...@gmail.com <mailto:sagmx.m...@gmail.com>>
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
========================================
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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