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

[sa]

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

So your advices are welcome.

SA


2011/3/28 sa <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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
>>
>>
>
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