[gmx-users] [ defaults ] and nonbonded

[Mark Abraham]

You've got a test case that shows your tables do what you think they do,
right? I would vary this setting and expect to see no effect.

Mark
On Jun 12, 2013 10:03 AM, "Steven Neumann" <s.neumann08 at gmail.com> wrote:

> Whether it would be that easy i will find it. I specified my own potential
> (not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed
> h(x) in my table 6th column.
>
>
> On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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
> >
> > --
> > ==============================**==========
> >
> > 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<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==============================**==========
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>