On 6/17/12 10:23 AM, Shima Arasteh wrote:
Hi all,
I simulated a protein in water. When I get its 20 ns trajectory and load it in
VMD, I see some bonds stretch suddenly and moves far strangely! Is this problem
because of the wrong structure of the protein? Or I may put some restrains on
system and solve this problem?
Anybody may suggest me in this about?
Please read this page in its entirety:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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