[gmx-users] Holes in the solvent!

Justin Lemkul jalemkul at vt.edu
Sat Oct 27 02:24:47 CEST 2012

On 10/26/12 3:25 PM, Arman M. Soufiani wrote:
> Dear Gromacs users,
> I am simulating a protein on a polymer surface for further adsorption free
> energy calculation.
> However, after performing the NVT run either for short or long durations I
> found out that couple of holes appear in the physiological saline solution
> (solvent)!!!
> Additionally, even proceeding with a long NPT run the holes are still
> present in the system.
> I would be thankful if you could direct me what could be source of such a
> strange outcome.

That sounds very odd, but perhaps your unit cell is not sufficiently solvated to 
start with.  If you have voids, you may have available volume.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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