From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Fri May 05 2006 - 15:46:06 CDT
Your system is probably just fine the way it is. Check the other side
of the box that your protein is sticking out of. There should be a
little hole where there is no water due to the presence of the periodic
replica of your protein (not shown, but it can be if you use VMD). NAMD
doesn't wrap molecules that are connected by bonds (a rather nice
feature most of the time). Look up the minimum image convention and
periodic boundary conditions in any text on MD if you have any other
questions.
-Sterling
Shirley Li wrote:
> Dear NAMD expert,
>
> As my MD simulation goes along (very long), several residues of the
> protein move out of water box. Is it appropriate to simply shift the
> box of water, and then minimize the entire system? Is there good
> solution with NAMD tools? In my script file, both wrapAll and
> wrapNearest are turned on.
>
> Any comments/info will be greatly appreciated.
>
> Shirley
>
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