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
--
========================================
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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