[gmx-users] Re: Holes in the solvent!
Dr. Vitaly Chaban
vvchaban at gmail.com
Mon Oct 29 15:15:04 CET 2012
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
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
> On Mon, Oct 29, 2012 at 1:20 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
>> >> 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
>> gmx-users mailing list gmx-users at gromacs.org
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users