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

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 28 14:13:44 CEST 2011


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.mail at gmail.com <mailto:sagmx.mail at 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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se



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