[gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

[Dallas Warren]

Just want to check that this should be taking as long as it is
(expected behaviour etc), for grompp to generate the tpr when nrexcl
is large.

I have a long straight chain molecule with 38 atoms that are
generating RDFs for, so need to change the [ moleculetype ] nrexcl to
exclude atoms within the same molecule from the generated RDFs.
Initially set nrexcl to 37, ran grompp to get the tpr, and it was
taking a loooong time and consuming significant amounts of memory.
Killed it and ran a few tests with increasing values and it is pretty
much instantaneous up until about 25.  Each increase after that
increases the time it takes in the " excluding ## bonded neighbours
molecule type '####' " step.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
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When the only tool you own is a hammer, every problem begins to resemble a nail.