[gmx-users] About periodic image of system.......

Justin Lemkul jalemkul at vt.edu
Sun Nov 11 16:00:40 CET 2012

On 11/11/12 4:51 AM, rama david wrote:
> Hi justin ,
> Thank you a lot for your explaination.
> My opinion  on the working of g_mindist -pi is that when it shows the
> distance between two atom
> of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it
> periodic image, and it is the violation of pbc.
> Is these is right??? ( That is the shortest Periodic distance should be
> larger than vdw cut off 1.4 )

This is correct, when considering a single molecule, i.e. it can't see itself. 
If you have two proteins, and you choose the blanket "Protein" group, you 
haven't determined anything, because now the calculation involves multiple 

> If it is right, g_mindist say that  The shortest periodic distance is
> 0.154938 (nm) at time 16162 (ps),
> between atoms 223 and 3270
> This is less than 1.4 then Why it is not problem..???

Because they're in separate molecules.  Did you ever do as I suggested and 
visualize this frame?  It will be immediately apparent that there is no problem. 
  Please refer to textbooks or even simple Google searching for explanations of 
the minimum image convention.  As I said, it is described in almost every 
reference text.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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