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

Chetan Mahajan chetanvm10 at gmail.com
Sat May 31 01:41:20 CEST 2014


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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