[gmx-users] Re: atoms jumps from its native position in protein

[Justin A. Lemkul]

Parthiban Marimuthu wrote:
> Hi
> i am trying to study protein-ligand interaction.
> at the end of the simulation, the visualization via- VMD shows, some of 
> the atoms suddenly jumped from its place to another space for a short 
> time and comes back to its position connected by huge lines. i dont have 
> any idea what is the real technical term to describe that.
> i am not sure where i am making mistake.
> could any one suggest this how to tackle this problem.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

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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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