Simulation results from NVT has a cavity

From: Xingcheng Lin (
Date: Sat Oct 19 2013 - 13:49:12 CDT


I met with one problem with NAMD all-atom explicit solvent simulation with
PBC on.

After done with the simulation, I found my movie in VMD is quite strange.
Firstly, the protein can move out of the water and secondly, there will be
a cavity in the water which has the similar size of the protein.

I guess this is resulted from the PBC, since each time there is cavity, the
protein is kind of stepping out of the box. I am worried about in that
situation, is the protein still being surrounded by water? Additionally,
the cavity seems not exactly matching the mirror of the protein, should I
be worried about that?

Many thanks,


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