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

[sa]

>
> OK, Pr van der Spoel,
>

So what is the correct way to obtain LJ C6 and C12 values given in the [
atomtypes ] and in the [ nonbond_types] sections of ffnonbonded.itp if I
have only the sigma and epsilon values.

If understand well [ atomtypes ] section give the comb-rules for the atom
with itself, correct ? And the nonbond_types section, the comb-rules with
the other atoms types.

So if  I take into account only the OM atom, as an example, why I obtained
different values for C6 and C12 terms in the [ atomtypes ] section.

Thank you again for your help.

SA


> ------------------------------
>
> Message: 2
> Date: Mon, 28 Mar 2011 14:13:44 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re: mathematical expression to obtain the C6
>        and     C12 LJ terms for the GROMOSXX ff family
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D907B78.20105 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
> >
> >         ========================================
> >
> >
> >
> >
>
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