[gmx-users] Box size to be considered in editconf

Justin Lemkul jalemkul at vt.edu
Fri Apr 27 21:02:16 CEST 2018

On 4/27/18 1:36 PM, SHYANTANI MAITI wrote:
> Dear all,
> What should be the size of a cubic box in the command editconf for
> simulating a protein-protein complex consisting of 500 residues altogether?

Depends entirely upon the geometry of the protein itself. The box size 
for a globular protein will be totally different from an elongated one. 
Use the -d flag to set a suitable buffer size and let editconf work its 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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