[gmx-users] see some line in vmd

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 26 01:36:02 CEST 2008

Morteza Khabiri wrote:
> Dear gmx user
> I have a box which contain protein and solution. Before running I
> minimized it very well and also system is running. After 2 ns when I saw
> the trajectory in vmd I saw that ther is some lines like bondes in the
> system. eg, between oxygen group of one water molecule in one part of box
> with hydrogen atom of other water molecule in opposite part.
> what do you think about this event?

One of two possibilities:

1. VMD is trying to be too smart.  The program determines "bonds" from the 
distances between atoms.  If atoms come within a "bond" distance, it displays it 
as such.

2. That is actually the same water molecule, careening across the system and is 
about to cause an explosion.  Be mindful of LINCS warnings.


> thanks
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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