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

Dallas Warren dallas.warren at monash.edu
Thu Sep 28 01:02:54 CEST 2017

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
When the only tool you own is a hammer, every problem begins to resemble a nail.

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