[gmx-users] Protein Complex simulation

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 19 20:48:21 CET 2011

Saba Ferdous wrote:
> Dear Justin, 
> I need to ask you that when we simulate 2 proteins and if the md.trr 
> show both protein quite far then what can be inferred from this when the 
> complex was simulated for 1ns.

If there was a protein complex at the outset of the simulation, you are probably 
observing a consequence of periodic boundary conditions.  1 ns is too short to 
observe anything useful, particularly a complete dissociation of a well-formed 
protein complex.



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


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