[gmx-users] box size and pbc

Daniela S. Mueller d.s.mueller at rug.nl
Thu Feb 9 23:57:01 CET 2006

Mark Abraham wrote:
> 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.

if the termini interact through the periodic boundary, the box is 
clearly too small. neutralising the termini is just a cosmetic solution, 
and maybe you don't want to change your system like that.

>> 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.

if your protein expands during the run, you either have to adjust the 
system by increasing the box size; or if you can anticipate this, start 
with a larger box to begin with.



Daniela S. Mueller

Diplom biologist

-Molecular Dynamics Group, UQ -

School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane

Phone: +61-7-33653732

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm


- MD group, RuG -

Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Email: d.s.mueller at rug.nl

Website: http://www.rug.nl/gbb/md

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