[gmx-users] Creating a box of water with density 1000 g/l
jalemkul at vt.edu
Thu Sep 10 22:56:48 CEST 2015
On 9/10/15 4:44 PM, Ebert Maximilian wrote:
> Hi there,
> I am wondering if there is a better way to create a box with water of a certain size than:
> gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512
> To get a density of roughly 1000 g/l i would need to add 512 molecules in such a box. But the script only adds 502. I could play with the scale parameter but sometimes I have problems during minimization with messages like:
> Water molecule starting at atom 1465 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
The density will anyway be dictated by the water model itself; none of the
common ones achieve exactly 1000 g/L. In principle, you could expand the box
very slightly, then re-size the box and simulate with NVT (thus constant
density), but at that point you're really manipulating the outcome, and I don't
know why you would need to go to such lengths.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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