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

[Justin A. Lemkul]

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 <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
> 
>         ========================================
> 
> 
> 
> 

-- 
========================================

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

========================================