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

Dr. Vitaly Chaban vvchaban at gmail.com
Mon Oct 29 13:20:26 CET 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

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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