[gmx-users] Strange behaviour of bonds

[Justin A. Lemkul]

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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