[gmx-users] Coulomb interactions

Swarnendu Tripathi stripat1 at kent.edu
Tue Mar 15 04:01:45 CET 2011

Thank you very much. I thought gromacs should do that but also a very useful
suggestion for checking that.


On Mon, Mar 14, 2011 at 9:54 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> On 15/03/11, *Swarnendu Tripathi * <stripat1 at kent.edu> wrote:
> Hello everyone,
> In gromacs when the Coulomb interactions are calculated are they calculated
> for the all atom pairs or only for the charged atoms pairs?
> GROMACS notices atoms with zero charge and does not put them into lists
> scheduled for evaluating charge-charge interactions. Similarly for zero LJ
> parameters.
> If the Coulomb interactions are not calculated only for the charged atoms
> then how can I modify the gromacs to do that. In my system I have only 27
> charged atoms  and I want gromacs to calculate  the Coulomb interactions
> only for these atoms. I am using gromacs 4.0.7.
> Obviously, this is only an efficiency issue, and GROMACS already takes care
> of it. You could see that this is true by making all of your "uncharged"
> atoms have charge 0.000001 and observing the increase in run time. You can
> also see this from the breakdown of computation time at the end of your .log
> file. There will be significant time spent doing LJ-only loops, and less
> time doing LJ+Coulomb loops.
> Mark
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