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

[Josip Lovrić]

Hello,

I am also interested in tabulated potentials and I am working to implement
it in my program.
I am interested do you think is it possible to put parameters (A, B, C) in
to the functions h(r) and and g(r)
and give value with parameters in the table and in the topology just set
parameters 1. In that way we do not care
does potential have LJ or Buckingham form. We give in table just numbers
and GROMACS interpolates  them so I
think for him is the same.

Best,
Josip


2014-05-29 20:21 GMT+02:00 Chetan Mahajan <chetanvm10 at gmail.com>:

> I forgot to say, but I look forward to hearing from both of you, with any
> comments on my understanding.
>
> Thanks
> Chetan
>
>
> On Thu, May 29, 2014 at 12:51 PM, Chetan Mahajan <chetanvm10 at gmail.com>
> wrote:
>
> > Hi Mark and Justin,
> >
> > File written by Gareth Tribello and attached to the end of following page
> > on GROMACS site discusses how one can specify buckingham interaction for
> Na
> > Na and Cl Cl while still specifying Lennard-Jone interaction between Na
> and
> > Cl. (page last modified on 9th Feb 2014 by Justin.)
> >
> >
> >
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials#Constructing_the_Table(s
> >
> >
> > File by Gareth Tribello mentions example of NaCl, where interaction Na Na
> > and Cl Cl is buckingham, whereas interaction Na Cl is LJ. But it's not
> > clear what should one specify nbfunc and comb-rule as, in a .top file.
> >
> > Also, let me share in the following, paragraph from section 6.9.2 of
> > Gromacs manual 4.6.5:
> >
> > "If you want to have different functional forms between different groups
> > of atoms, this can be set through energy groups. Different tables can be
> > used for non-bonded interactions between different energy groups pairs
> > through the .mdp option energygrp-table (see sec. 7.3). Atoms that should
> > interact with a different potential should be put into different energy
> > groups. Between group pairs which are not listed in energygrp-table, the
> > normal user tables will be used. This makes it easy to use a different
> > functional form between a few types of atoms."
> >
> > All of this does point out that one can mix LJ and buckingham amongst
> > different pairs of atoms. e.g. A and B could interact via LJ potential,
> > whereas A and C (say C is bonded to B) interact via buckingham potential.
> >
> > Thanks
> > Chetan
> >
> >
> > On Thu, May 29, 2014 at 12:51 AM, Mark Abraham <mark.j.abraham at gmail.com
> >
> > wrote:
> >
> >> Hi,
> >>
> >> I do not think there is any ability in GROMACS to mix LJ and Buckingham.
> >> Each particle can have only one set of non-bonded parameters, so there
> is
> >> no sensible way to express the interaction between the sets of atoms
> >> natively using each type of interaction.
> >>
> >> Mark
> >> 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?
> >> >
> >> > 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.
> >>
> >
> >
> --
> 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.
>