Re: protein moves away from water box

From: Shirley Li (
Date: Fri May 05 2006 - 18:38:38 CDT

Hello Sterling,
 Thank you so much for your kind help. I have two further questions:
 1) How to display a periodic replica in VMD? I went through the menus but didn't find it.
 2) For the situation I have, how do I know the system is still fine, or it needs to be recentered?
 Thanks a lot again for your help.
 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
 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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