[gmx-users] Holes in the solvent!

Christopher Neale chris.neale at mail.utoronto.ca
Tue Oct 30 02:09:05 CET 2012

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.


-- 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
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


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