[gmx-developers] Suggestion: move bonded forces in mdrun

[Carsten Kutzner]

Hi there,

I wonder if it is possible to move the calculation of the bonded forces
(calc_bonds) before the do_pme routine in mdrun. This way, one could
achieve slightly better scaling when using PME in parallel runs, in
particular for systems that consist of a single large protein in water.

In the current code, where the bondeds are evaluated after PME, a single
CPU calculates the bonded forces for the big protein while the
others are already finished and waiting. If the bondeds were before PME,
one could give this CPU somewhat less atoms via the -load "..."
option in grompp, so that all CPUs enter the PME routine at the same
time. This would also enhance the potential speed gain for future dynamic
load balancing.

As I see it, this would only require a slight change in the force.c
routine.


   Carsten



---------------------------------------------------
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
eMail ckutzne at gwdg.de
http://www.gwdg.de/~ckutzne