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

[Chetan Mahajan]

Hmm. Gareth Tribello does say on the page 5 of that document:

 As for the cross terms, unless you have specific reason to believe that
gromacs will mix the terms correctly using mixing rule 1, you must provide
these explicitly in the [ nonbond params ] section immediately after the [
atomtypes ] section as follows:

I do not know why he thinks gromacs may not mix the terms correctly.
Thanks
Chetan

On Sat, May 31, 2014 at 8:43 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> I don't know. Confirmation is best done by testing it. Use mdrun -rerun and
> vary parameters and tables until you are satisfied you understand how it
> works.
>
> Mark
> On May 31, 2014 1:44 AM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:
>
> > Here is one more thing (hopefully last!):   If you have 8 energy groups,
> > there are lot of cross terms as you see. Some of these cross terms have
> to
> > be described by specific tables for each of those pairs. However, many
> > other pairs do not need specific tables, so a general table.xvg (not
> > specified by energygrp-table option), which is for pure LJ interaction in
> > my simulations, would suffice. Now, is it mandatory that I need to
> > explicitly provide LJ parameters for all of these remaining pairs (too
> many
> > !) or Gromacs will calculate those using combination rule and then apply
> > table.xvg, as it is intended to apply to a non-specific pair? I feel
> > Gromacs should be able to calculate cross term and apply table.xvg,
> without
> > the need to enter C an A for that pair explicitly as an additional term
> in
> > topology file. I need to confirm.
> >
> > Thanks
> > Chetan
> >
> >
> > On Fri, May 30, 2014 at 2:38 AM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Yes. Three parameters are needed for nbfunc 2 in order to use the few
> > > kernels that implement Buckingham; using a Buckingham-shaped table with
> > > nbfunc 1 is not "using Buckingham" from the point of view of how many
> > > parameters grompp will expect.
> > >
> > > Mark
> > > On May 30, 2014 8:19 AM, "Chetan Mahajan" <chetanvm10 at gmail.com>
> wrote:
> > >
> > > > 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
> > > > > > --
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