[gmx-users] Holes in the solvent!

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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