[gmx-developers] use multiple tables for pair interactions

Dongsheng Zhang dong at pampas.chem.purdue.edu
Mon Jul 17 15:06:16 CEST 2006

Dear Hess,

Thank you very for your reply.

On Mon, 2006-07-17 at 08:46 +0200, hessb at mpip-mainz.mpg.de wrote:
> > Dear GMX developers,
> >
> > I want to use a coarse grained model, which includes several tabulated
> > potentials for pair interactions, but no COUL term. Currently Gromacs
> > can only read one table for pair interactions. Could you please help me
> > modify the source code such that Gromacs can support multiple tables for
> > pair interactions?
> >
> > Another way I am thinking to solve my problem is to fool gromacs to take
> > advantage of COUL term in VDWs table since my coarse grained model does
> > have COUL term. In other words, I put all pair interaction values in
> > COUL term in the regular VDWs tables (Gromacs can read multiple VDWs
> > tables), so when gromacs wants to calculate pair interaction energys,
> > gromacs will use the codes for calculate COUL energy by reading VDWs
> > tables. Here I need to modify the source code to change the flow. If you
> > think this is a good idea, could you please shine a light o tell me
> > where I need to modify in source code (where gromacs calculate the
> > nonbonded energies and forces)?
> Changing the code is somewhat involved,
> as the pair interactions are bonded interactions and they
> are therefore not assigned to charge groups.
> I have used the other option you mention several times.

Do you mean you to take advantage of COUL term in the table.xvg? I am
confused by your second last paragraph.

> You actually have three tables at your disposal:
> two for LJ (usually 1/r^6 and 1/r^12) and Coulomb.
> So if you can have three independent functional forms,
> if you can choose your charges appropriately.
> The strength of the interactions can then be scaled
> with C6, C12 and the charges.
If I will use COUL term in table.xvg to calculate the pair interaction,
I have to set all my charge as +1, right? In my carse-graied model,
there is not explicit sigma and epslong, the interaction energies are
completely tabulated so c6 and c12 will be +1 for regualr VDWs, same as
pair interations.

> But note that the Coulomb interactions always contain
> a factor f*q1*q2 (see the manual).

This the reason that I think I have to set q1 and q2 to be +1;

> If you need three tables (with two you can use only LJ),
Here I am confused. What do you mean "three tables"? To my
understanding, each table.xvg has three terms (COUL, c6, c12) with total
of 7 columns. 
> you should make all Coulomb tables for the nonbonded
> interactions zero so you can use the charges for the pair
> interactions only.
Sorry I don't know what you mean. If I want to use COUL term to
calculate pair interactions, I can't make all Coulomb tables for the
nonbonde interactions zero.

> Note that this strategy only works when you do not need
> different interaction distances, such as for instance
> different sigmas would require for LJ.

I think we can make such a table that c6 and c12 are unity, so there are
no explicit sigmas.

> Berk.
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.

More information about the gromacs.org_gmx-developers mailing list