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

[Mark Abraham]

Hi,

I'm sure we have opportunities to improve this code - please do file a
redmine issue with repro inputs so we can profile and see!

Thanks,

Mark

On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
> numbers.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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