[gmx-developers] use multiple tables for pair interactions

Berk Hess hessb at mpip-mainz.mpg.de
Mon Jul 17 15:13:51 CEST 2006

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 
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 
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.


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