[gmx-users] Re: Holes in the solvent!

[Arman Mahboubi Soufiani]

Dear Friends,

Thank you for your kind and informative responses. As Dr. Chaban noted, I
checked the density and it was roughly 880 gr.cm-3 which seems low!

I greatly appreciate your further helps.

Best Wishes

Arman

On Mon, Oct 29, 2012 at 1:20 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> >> 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
>
>
> You must compare the simulated density with the experimental density.
>
> There is no other way to conclude if your holes are genuine or not in
> this kind of matter.
>
>
> Dr. Vitaly V. Chaban
> MEMPHYS - Center for Biomembrane Physics
> Department of Physics, Chemistry and Pharmacy
> University of Southern Denmark
> Campusvej 55, 5230 Odense M, Denmark
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