[gmx-users] help please @User-specified potential functions

[Chetan Mahajan]

Thanks. So let me rephrase so that I get your point:

I reread the document by Gareth. As described in section 2 (changing the
form of global interaction), nbfunc is set to 1, even if potential is of
6-9 form instead of 6-12 form of Lennard Jones. Now, even for buckingham,
only C and A need to be provided, since B can be clubbed with function of r
i.e. exp(-B*r), as you mentioned in the beginning of last email of yours
(although the *source of the confusion was the note 1 on the bottom of page
2 of this document*, which says 3 parameters A, B and C need to be provided
for buckingham). Thus, nbfunc=1 should work even if some pairs interact via
buckingham while others by LJ.

Please comment.

Thanks
Chetan


On Fri, May 30, 2014 at 12:02 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On May 29, 2014 2:28 AM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:
> >
> > Dear All,
> >
> > I just came across this fantastic capability of Gromacs, user-specified
> > potential functions, which can let me use LJ potential for some atom
> pairs
> > whereas Buckingham for some others. However, I have a doubt about
> topology
> > file construction, even after reading a document by Gareth and going
> > through earlier posts on this mail-list. I would be highly obliged if
> > anyone can help:
> >
> > Specifically, since I have LJ and buckingham both, do need to repeat
> > statement mentioning nbfunc ( and combination-rule) in .top file? e.g.
> > nbfunc=1 followed by LJ parameters  C and A for the concerned pairs and
> > then nbfunc=2 (and whatever combination rule) , followed by buckingham
> > parameters C, A , B for concerned pairs in the .top file?
>
> Gareth's approach relies on absorbing the extra parameter for Buckingham
> into h(r) of the table and specifying which tables are used by which pairs
> of atom types. That should work, but IIRC is capped by the allowed number
> of energy groups, probably 64. My earlier point was that GROMACS can only
> do the same thing with the parameters for the two interaction types right
> up to the point the table is used, so you must express in the topology the
> right values for whichever nbfunc value you choose as convenient. You can't
> choose a second value for nbfunc anywhere. Depending on your values and
> combination rule, you might need to absorb a scaling factor into g(r) or
> h(r), too!
>
> Mark
>
> > Thanks a lot!
> >
> > regards
> > Chetan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>