[gmx-users] gmx insert-molecules question

[Mala L Radhakrishnan]

Thanks!  (and sorry about all the typos in my original email -- just
re-read it and saw it was barely intelligible!)

M

On Thu, Jul 25, 2019 at 4:25 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/25/19 4:11 PM, Mala L Radhakrishnan wrote:
> > Hi,
> >
> > I am trying to crod snapshots with multiple copies of a molecule.  When I
> > run gmx insert-molecules and I have a box of a certain size, does it make
> > sure that there is no overlap of molecules even considering pbc?  What I
> > mean by this is if I do a trjconv on the resulting  crowded snapshot,
> using
> > -pbc atom, will any of the atoms/molecules overlap?  Or maybe another way
> > of saying it is, if a molecule, when places, falls partially outside the
> > box does it ensure that another molecule wouldn't overlap with the
> periodic
> > image of that first molecule?
>
> Yes, the insert-molecules code uses PBC in its neighbor searching.
>
> -Justin
>
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-- 
Mala L. Radhakrishnan
Associate Professor of Chemistry
Director, Biochemistry Program
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981