Re: protein moves away from water box

From: Sterling Paramore (
Date: Fri May 05 2006 - 19:00:01 CDT

1)For VMD: go to graphics, then representations, then click on the
periodic tab. There you can set in which directions you want the
periodic replicas to be drawn. If you're using a .dcd file, then it
should work just fine. If it's a pdb file you might have to manually
set the cell vectors using the tkconsole and the command: molinfo top
set a 10 (which sets the cell vector in the x direction to 10 angstroms,
likewise for the other directions).

2) Again, read about periodic boundary conditions (I assume you're using
periodic boundary conditions since you mentioned a box and the wrap
commands). With periodic boundary conditions, there is no such thing as
outside of the box and the center of the box is arbitrary and
meaningless. Allen and Tildesley have a great illustration (fig. 1.9),
which is almost identical to the figure I see in the first link I get
from google when searching for "periodic boundary conditions".


Shirley Li wrote:

> 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.
> Shirley
> ===================================
> 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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