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.
Mark
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