Somehow a water cavity formed during the NVT equilibration

User discussions
1

GROMACS version: 2019.4

I was trying to simulate a system consisting of the carbon nanotube and graphane. When I conducted the NVT equilibraition, I saw a water cavity occuring near the edge of the box. It was still there after 2 ns (haven’t tested for longer). It is very odd. Anyone knows why? BTW, flexible waters were used during energy minimization and the NVT process.

Also since I am going to freeze the carbon nanotube and graphane during the whole simulation, I assume pressure equilibration will not be applicable. In that case, without box rescaling during NPT, is the concentration of the salinity solution the same as the one assigned during “gmx solavte” and “gmx genion”?

vmd

2

If the interior of the CNT was dehydrated (partially or fully), then water molecules will flood into that void, leaving behind another void. You may have to add more water to the system while building the initial coordinates (or just add more water to this system, minimize, and re-equilibrate).

3

It all makes sense! Thanks a lot. That is really helpful.