GROMACS modification: Yes/No
Here post your question
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?
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?
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.