[gmx-users] Table Potential for molecules with partial charge on atoms

Alireza Moradzadeh a.mrdzd at gmail.com
Thu Feb 25 03:30:36 CET 2016

Dear All,

I am trying to use gromacs for molecules with three beads and one bead my
molecules have partial charge on each bead.

When I simulate gromacs without table by just using LJ parameters and PME
my system works well. But when I insert table for interactions and using
PME my system blows up. I think this problem is related to charges because
my system works well when I put charges to zero, I face no problem.

Do you have any suggestion on how to use table with charges on my atoms for
each molecules?

More info:

1. I use LINCS to keep bonds and angles rigid for both table and LJ.
2. Molecule CA has three beads (Me, Ar, and Bu) with partial charges of
(0.2 0.6 0.2) ;
3. Molecule AN has one bead (AN) with charge -1;
4. Using LJ parameters with Col. (PME)  my system works well
5. Using table with following group: Me, Ar, Bu, and AN and 10 energy group
tables my system blows up, unless I put charges to zero.

Question: how to use table with energy group within the same molecules?

If you need more information let me know.
And, if it is not possible to do this work with GROMACS can I use LAMMPS or
it will face the same problem.

Best Regards,
Alireza Moradzadeh

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