[gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?
ddhabal at seas.upenn.edu
Mon Mar 12 17:29:37 CET 2018
Could anyone of you help me regarding the aforementioned problem. It would
be very nice of you.
Thanks in advance.
On Sat, Mar 10, 2018 at 1:30 PM, Debdas Dhabal <ddhabal at seas.upenn.edu>
> Dear Mark,
> 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 time.
> 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
> same time.
> I hope I am able to make my question more clearer than before. Thanks
> again for your help.
> With regards
> 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
>> > 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
>> > 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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> Debdas Dhabal
> Postdoctoral Researcher.
> SEAS, Department of Chemical and Biomolecular Engineering,
> The University of Pennsylvania, Philadelphia, PA 19104, USA.
SEAS, Department of Chemical and Biomolecular Engineering,
The University of Pennsylvania, Philadelphia, PA 19104, USA.
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