[gmx-users] box size and pbc

Yang Ye leafyoung81-group at yahoo.com
Thu Feb 9 20:01:42 CET 2006

Wang Zhun wrote:
> Hi,
> Editconf command generates a box for further solvation. When no definite box size and type are set, it will constructs a cubic box which might be the smallest to contain the solute, as far as I know.I set -d with 0.6 and full PBC for this box to simulate peptides folding.With VMD I found in one case a peptide moved out of the box while in another MD the two termini of the peptide both stretched out of the box.
Solute slowly drifting during MD is quite fine.
>  For the 1st one I think the PBC is ok, but what about the 2nd case if the two termini point to the opposite box sides? It seems there is no post on this editconf option. I know I'd better choose a large dodecahedron box but I just wonder if this box should be ok to perform MD with PBC.
> Thanks!
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Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Tel: 6316-2884

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