[gmx-users] 2 amino_acid outside the box before animation in ngmx

[Justin Lemkul]

On 1/22/13 9:35 AM, Devika N T wrote:
> Dear all
>
> I have performed 1ns simulation for my protein (148 aa) complexed with calcium
> ion.
> After the generation of 1ns files, I have given *"ngmx"* to view the protein
> .
> But I can see 2 amino acids residues out of the box before giving the
> "animation" option in "ngmx"
>
> While giving the "animation"  option at around 980ps th 2 residues are
> going inside the box.
>
> Box shape given : octahedron with "2" and centered.
>
> What could be the reason..

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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