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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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