[gmx-developers] use multiple tables for pair interactions

Dongsheng Zhang dong at pampas.chem.purdue.edu
Mon Jul 17 17:22:28 CEST 2006

On Mon, 2006-07-17 at 15:13 +0200, Berk Hess wrote:
> Dongsheng Zhang wrote:
> >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.
> >>    
> >>
> I'll try to word it differently.
> You apparently want to use different forms of pair interactions for 
> different
> atom pairs in the [ pairs ] section of your topology.

> Without changing the code you can only use the 3 functional forms
> that are supplied in tablep.xvg.
> If you need 2 functional forms, things are easy since your can indepently
> modify the 2 functions normally used for 1/r^6 and 1/r^12.
> If you need more than 3 you are out of luck.
> If you need 3 functional forms, you can use the electrostatics part of 
> tablep.xvg.
> Here you need to take into account the factor f*q1*q2 in the potential.
> Also the electrostatics functions in all table_?_?.xvg files should be zero,
> as otherwise you will get unwanted non-bonded interactions.

Dear Berk,

To my understanding, one tablep.xvg can only take care of one type ( two
specific atoms) of pair interaction, even though there are three
functional forms. In my case, The pair interaction potential does not
include COUL term, and the potential is completed tabulated (means there
is no formula e.g. 1/r^6), so I will only use one functional form
(attractive or replusive part) and  C6 and c12 are unities.

Now I give you my case. I try to use a coarse grained model for
PEO-PPO-PEO triblock polymers. There are three different pair
interactions, namely, PEO-PEO, PPO-PPO, PEO-PPO. I thought I need three
tablep_*_*.xvg files for them. Could you please kindly tell how I can
change tablep.xvg to calculate those three different types of pair
interactions without modifying the source code? 

In some sense, I think maybe my question is not so clear to you, so I
can't get your answer. I hope you can understand my question now.

Thank you very much for your help!


> 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