[gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?
ddhabal at seas.upenn.edu
Sat Mar 10 19:30:32 CET 2018
Thanks so much for your prompt reply. I had gone through that manual and I
was able to use two different non-bonded potential for two different energy
groups using table potential. But my question is a bit different. May be I
was not able to make my question clear. I know the fact that by using table
file I can use two different non bonded potential but what I wanted to ask
whether it is possible to use table file only for user defined potential
and not for which Gromacs already have predefined potential at the same
Let me make it more clear. I have a system of solute in water. I want to
use table file for only solute-water interaction and want to let the
Gromacs take LJ potential for water-water interaction (ie. I don't want to
explicitly supply water-water interaction through Table file). In another
way one can ask if I put *"vdwtype=User"* then is it *mandatory* to give
non-bonded potential for both solute-water as well as water-water
interaction through Table file only, or one can only use Table file for
solute-water and Let the Gromacs take its predefined LJ potential form for
water-water interaction (as in case of vdwtype = Cut-Off case). So
basically using Gromacs predefined potential and table potential at the
I hope I am able to make my question more clearer than before. Thanks again
for your help.
On Sat, Mar 10, 2018 at 7:52 AM, Mark Abraham <mark.j.abraham at gmail.com>
> Yes, if you check out the documentation of tabulated non-bonded
> interactions in the reference manual, you will see that you can apply
> different tables for particles when drawn from different energy groups.
> On Sat, Mar 10, 2018 at 1:06 AM Debdas Dhabal <ddhabal at seas.upenn.edu>
> > Hello everyone,
> > This question may be very simple to most of the Gromacs user. I wonder if
> > Gromacs allow us to use both user-defined non-bonded potentials (Table
> > potential) as well as Gromacs predefined potential at the same time. For
> > example, if I have a system with a solute in a solvent and for
> > solvent-solvent nonbonded interaction, I want to use Gromacs defined LJ
> > potential but for solute-solvent nonbonded interaction, I want to use a
> > custom potential using a Table format. I know that solvent-solvent
> > interaction can also be incorporated in the Table file and we can run
> > Gromacs successfully, but I want to use Table potential only for which
> > Gromacs does not have predefined form. Is it possible ?. If so, I would
> > be grateful if someone could suggest me to how to do that?.
> > I will appreciate all your valuable inputs. Thanks so much in advance.
> > --
> > Debdas Dhabal
> > Postdoctoral Researcher.
> > SEAS, Department of Chemical and Biomolecular Engineering,
> > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> > --
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