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

[Mark Abraham]

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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