[gmx-users] Electrostatic potential

[Justin A. Lemkul]

ithu wrote:
> I can't figure out how to put the coulombic potential only between 
> residues in chain A and residues in chain B, but not between residues 
> that are in the same chain.
> 

You could look into energygrp_excl, but that will exclude *all* non-bonded 
interactions, not just electrostatics.  Otherwise, you may have to use tabulated 
potentials or adjust the value of nrexcl in the topology (which will also affect 
vdW, not just electrostatics).

-Justin

> Thanks,
> Esteban
> 
> 2010/8/28 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     ithu wrote:
> 
>         Hi everybody,
> 
>         I want to apply a coulombic potential between charged residues
>         in a coarse-grain model, but between residues that belong to
>         different chains of a protein complex. Both chains are name as
>         molecule A and molecule B in the topology file.
> 
> 
>     What specific problem are you having?  In order to get useful
>     advice, you'll have to describe exactly what you're doing and why
>     it's not working when you think it should.  A variety of models for
>     treating electrostatic interactions are available in Gromacs.
> 
>     -Justin
> 
> 
> 
>         Thank you very much,
>         Esteban
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================