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

[Chetan Mahajan]

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
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