[gmx-users] Re: Tabulated potentials and normal nonbonded interaction at the same time
schlesi at uni-mainz.de
Thu Sep 16 11:48:36 CEST 2010
first, thank you for you're answers.
I looked more into the stuff.
I think i would use the following setup:
Since the CG-solvent is uncharged, i can use the normal
coulomb-interaction (PME) for the system.
For the vdw-part, i would use 'vdw_type=user' and:
energy_grps = CG Mol
energygrp_tables = CG CG (CG self-interaction) CG Mol (CG-Molecule
(CG = CG-solvent; Mol=Molecule)
So i would need two tables (for each interaction one).
With this i should get all the vdw-interaction where the CG-solvent is
But since i need normal vdw-interactions for the Molecule
self-interaction, i would need in the .mdp-file
'vdw_type = user' AND 'vdw_type = cut-off'
Or am i wrong (hope so)? Because the only way i can think of to solve
the problem, would be that i make for every vdw-self-interaction of the
Molecule an own table, which wouldn't be good (since i read somewhere
that tables are slower then to calculated the interaction normally).
So how could i solve the problem, or this there no problem because i
didn't understand the whole stuff correctly (seems so because of Marks
>> > I think what you need to do is use multiple tables. So you
>> > have one
>> > table for your CG-solvent interaction with itself and then
>> > another one
>> > for your CG-solvent (uncharged) interactions. (This second table
>> > would then just a tabulated version of the Lennard Jones >interaction
>> > or whatever you are using.) This page might be of help:
>> > http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>While this would work, the key piece of information is that GROMACS
>will permit you to use different tables only for selected
>inter-energy-group interactions. So the OP needs suitable energy
>groups, and only one table. The other groups use the normal >interactions.
> > ciao
> > Gareth
> > On Wed, Sep 15, 2010 at 5:40 PM, Thomas Schlesier
> > <schlesi at uni-mainz.de> wrote:
>> > > Dear Gromacs-User,
>> > > i want to try to simulate an atomistic molecule with CG-
> > solvent (uncharged).
>> > > For the atomistic molecule i want to use the normal non-bonded
> > interactions,> but for the CG-solvent interaction with itself
> > and the molecule i need a
>> > > tabulated potential.
>> > > So my question is, is that possible to do in Gromacs?
>> > > I looked a little bit into the manual and it seems that
> > tabulated potentials
>> > > use the 'vdw_type' and/or the 'coulomb_type' keyword, which i
> > will need for
>> > > the normal interactions.
>> > > Greetings
>> > > Thomas
>> > > --
>> > > gmx-users mailing list gmx-users at gromacs.org
>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > > Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > > Please don't post (un)subscribe requests to the list. Use the
More information about the gromacs.org_gmx-users