[gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

[Debdas Dhabal]

Hello everyone,

Could anyone of you help me regarding the aforementioned problem. It would
be very nice of you.

Thanks in advance.

With regards
Debdas

On Sat, Mar 10, 2018 at 1:30 PM, Debdas Dhabal <ddhabal at seas.upenn.edu>
wrote:

> 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
> Debdas
>
> On Sat, Mar 10, 2018 at 7:52 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> 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.
>>
>> Mark
>>
>> On Sat, Mar 10, 2018 at 1:06 AM Debdas Dhabal <ddhabal at seas.upenn.edu>
>> wrote:
>>
>> > 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.
>> > --
>> > 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.
>>
>
>
>
> --
> Debdas Dhabal
> Postdoctoral Researcher.
> SEAS, Department of Chemical and Biomolecular Engineering,
> The University of Pennsylvania, Philadelphia, PA 19104, USA.
>



-- 
Debdas Dhabal
Postdoctoral Researcher.
SEAS, Department of Chemical and Biomolecular Engineering,
The University of Pennsylvania, Philadelphia, PA 19104, USA.