Water free areas

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#1

GROMACS version:
GROMACS modification: Yes/No
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Hi guys, I have a water free regions after performing simulations for my silica surface at different degrees of ionisation when viewing the structure on VMD? Is there a possible explanation for this?

I have omitted the silica surface and only show the counter ions and water for ease of view and the first image was at pH 5.6 in which the surface is negatively charged. The counter ions are in blue and do not seem to occupy the hole either. What could be the reason for this?

image

Here is another image at pH 7 and the hole is smaller but there are water free regions at the edge too. Why does this occur?

image

Could a possible explanation be that the water (solvent acts) as barrier in the MD simulations to prevent the counter ions from influencing the behaviour of the surface. Therefore, the water occupies regions that contain the counter ions and explain why the regions that are vacant is because there are no ions in those supposed holes, if you notice carefully.

Any help would be much appreciated.

#2

Do you run NPT or NVT?

#3

Hi,
did you equilibrate the system conditions (e.i. volume/pressure and temperature) before data production?
Alessandra

#4

I performed minimisation, and then equilibration and this is then followed by production.

#5

Equilibration Input Generation Options:

NVT Ensemble

Dynamics Input Generation Options:

NPT Ensemble

#6

So the production run is constant pressure?

#7

Yes, the pressure is constant.

#8

You are going to have to look closely at it with your own eyes, play the trajectories, and try to work out what is going on. Look at things like are they always there, so they move, how large they are, groups around them. Probably would need to run other simulations removing variables (ie some of the molecules/ions) to try and work out what is going on.