sukesh chandra gain wrote:
Dear All,
I am doing a simulation for ligand-enzyme complex in a octahedron box. I
have mentioned -c with editconf, but after energy minimization the
protein is placed at the top of the box. Could you please suggest me how
could I keep the protein at the centre of the octahedron box?
This is simply a visualization artifact. Use trjconv -pbc mol -ur compact to
"correct" your structure. But do be aware that this is simply a convenience for
visualization, in an infinite system (with PBC), there is no "center" of a box.
-Justin
Here are the details:
After
editconf>
Volume =283.195nm^3
System size : 6.852 5.060 7.638
genbex>
box_margin = 0.315
Removed 29370 atoms that were outside the box
grompp>
Using a fourier grid of 88x88x88, spacing 0.115 0.115 0.115
Thank You,
Regards,
Sukesh
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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