Re: Simulation results from NVT has a cavity

From: Kenno Vanommeslaeghe (
Date: Mon Oct 21 2013 - 12:25:58 CDT

You may want to look up some background information (for example in a
basic textbook) on what PBC is and what it does. After doing so, have a
look at the "Periodic" tab in VMD's "Graphical Representations" dialog
box. Also potentially of interest is VMD's PBCTools plugin.

On 10/19/2013 02:49 PM, Xingcheng Lin wrote:
> Hi,
> 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,
> Arrow

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