[gmx-users] Is there a way to omit particles with q=0 from Coulomb-/PME-calculations?

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 16 23:31:03 CET 2012

On 17/01/2012 4:55 AM, Thomas Schlesier wrote:
> Dear all,
> Is there a way to omit particles with zero charge from calculations 
> for Coulomb-interactions or PME?
> In my calculations i want to coarse-grain my solvent, but the solute 
> should be still represented by atoms. In doing so the 
> solvent-molecules have a zero charge. I noticed that for a simulation 
> with only the CG-solvent significant time was spent for the PME-part 
> of the simulation.
> If i would simulate the complete system (atomic solute + 
> coarse-grained solvent), i would save only time for the reduced number 
> of particles (compared to atomistic solvent). But if i could omit the 
> zero-charge solvent from the Coulomb-/PME-part, it would save much 
> additional time.
> Is there an easy way for the omission, or would one have to hack the 
> code? If the latter is true, how hard would it be and where do i have 
> to look?
> (First idea would be to create an index-file group with all 
> non-zero-charged particles and then run in the loops needed for 
> Coulomb/PME only over this subset of particles.)
> I have only experience with Fortran and not with C++.
> Only other solution which comes to my mind would be to use plain 
> cut-offs for the Coulomb-part. This would save time required for doing 
> PME but will in turn cost time for the calculations of zeros 
> (Coulomb-interaction for the CG-solvent). But more importantly would 
> introduce artifacts from the plain cut-off :(

Particles with zero charge are not included in neighbour lists used for 
calculating Coulomb interactions. The statistics in the "M E G A - F L O 
P S   A C C O U N T I N G" section of the .log file will show that there 
is significant use of loops that do not have "Coul" component. So 
already these have no effect on half of the PME calculation. I don't 
know whether the grid part is similarly optimized, but you can test this 
yourself by comparing timing of runs with and without charged solvent.


More information about the gromacs.org_gmx-users mailing list