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

Justin Lemkul jalemkul at vt.edu
Tue Oct 3 15:05:19 CEST 2017

On 10/2/17 11:14 PM, Dallas Warren wrote:
> Thanks for the reply Justin.
> I am just going to use the largest exclusion bond distance I can, then
> ignore the RDF of those beyond that distance.
> Seems curious to me (not actually understanding what grommp is
> generating) that the list is so large.  These are linear molecules, 38
> atoms, 60 molecules in total.

It generates a matrix of all possible exclusions, sorts them, then removes 
duplicates. So for nrexcl = 37 you need memory on the order of 37 * 37 * 60 * (2 
* sizeof(int)) - the factor of 2 for the atom numbers comes from the fact that 
you're actually allocating an array of type "sortable" which is a pair of atom 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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