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

[Dr. Vitaly Chaban]

On Mon, Oct 29, 2012 at 2:38 PM, Arman Mahboubi Soufiani
<armansoufiani at gmail.com> wrote:
> 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!

Dear Arman -

You did not mention the experimental density of your system.

Whereas we expect saline solution to exhibit the density of > 1000
kg/m3, we have no idea about your polymer composition and spatial
structure.

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




>
> 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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>