[gmx-users] box size and pbc

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 9 23:08:47 CET 2006

Wang Zhun wrote:
> 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.

This latter observation could be a problem. Now your termini might be 
closer to the periodic copies of other termini than you would actually 
want. If your termini are zwitterionic, you could be observing them 
attracting each other through space. If so, neutralise each with a 
counter-ion using genion.

You can also use trjconv after a simulation with the -pbc flag set 
appropriately to do what you want the system to do when it's periodic. 
See the manual/manpages.

> 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.

Larger is probably better, but neither cubic nor dodecahedron of 
comparable size should be a problem.


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