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

Thomas Schlesier schlesi at uni-mainz.de
Mon Jan 16 18:55:12 CET 2012

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 
(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 :(

Hope anyone could help.

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