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

Devika N T deviinfoz.an at gmail.com
Tue Jan 22 15:35:04 CET 2013

Dear all

I have performed 1ns simulation for my protein (148 aa) complexed with calcium
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..
Calcium ion is present inside the box only.

Please help me out.

 * Regards**
  N.T. Devika*

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