[gmx-users] Holes in the solvent!

Arman Mahboubi Soufiani armansoufiani at gmail.com
Tue Oct 30 06:46:39 CET 2012

Dear Chris,

Thank you for your directions. NaCl concentration in my system is 0.14 M
and I often visualize the whole system and can see the ions around the
system but not in crystal form!
Well, it sounds really strange to me! And I don't know if I proceed with
such a system, I get scientific results or not?!
I appreciate your further helps.

Best Regards


On Tue, Oct 30, 2012 at 4:39 AM, Christopher Neale <
chris.neale at mail.utoronto.ca> wrote:

> In addition to the comments of Dallas Warren, which seems quite possible
> and should be checked,
> are you sure that you are seeing real holes and not just salt crystals
> that look like holes when you render only
> the waters with VMD? I have found that, at NaCL concentrations above 1 M,
> lipid bilayers catalyze the formation
> of salt crystals when using TIP3P/4P water and the OPLS/AA-L force field
> for ions. These crystals looked a lot
> like vacuum holes to me until I visualized the salt.
> Chris.
> -- original message --
> 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.
> Best Wishes
> Arman
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