[gmx-users] [ defaults ] and nonbonded

[Justin Lemkul]

On 6/11/13 4:12 PM, Steven Neumann wrote:
> Dear Gromacs Users,
>
> I got really confused: In manual [defualts ]:
>
> "nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
> (Buckingham)"
>
> I want to use mdrun -table table.xvg with my own potential, which one I
> should choose?
>
> "gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4
> parameters from the pairtypes list. When parameters are not present in the
> list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that
> are not present in the pair list from normal Lennard-Jones parameters using
> fudgeLJ"
>
> I want to have all intramolecular atoms (within my chain) interacting (no
> exclusions) with each other from [ atomtypes ] in ffnonbonded.itp
> Does it mean "yes" with nrexcl =1 in my topology?
>
> And sth I also got confused:
>
> [ pairtypes ] are only 1-4 parameters or here I can specify parameters for
> all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also
> correspond to intra molecular interactions?
>

These topics are discussed frequently.  Please search the archive; surely you 
will find relevant topics.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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