[gmx-users] gmx insert-molecules question

[Mala L Radhakrishnan]

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?

Hope this question makes sense -- thanks!

Mala

-- 
Mala L. Radhakrishnan
Associate Professor of Chemistry
Director, Biochemistry Program
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981