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
--
========================================
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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