[gmx-users] gmx insert-molecules question

[Justin Lemkul]

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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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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