[gmx-users] genion deletion edges

David spoel at xray.bmc.uu.se
Mon Nov 22 20:34:59 CET 2004

On Mon, 2004-11-22 at 13:02 -0500, dsh2002 at med.cornell.edu wrote:
> Yes, genion puts it back into the box, but it deletes any atom that
> protrudes out of the box. (which I guess is necessary for the periodic
> boundary calculations?)
Are you sure? Please count the number of atoms...

> So my question now is, how far can the edge of the box be from the
> molecules in the system?  I believe in principle one would like to put the
> edges of the box as close as possible, but b/c my lipid bilayer has lipids
> that are not exactly normal to the axes and protrude out, I have to make a
> larger box that encloses the whole lipid.  So the result is empty areas on
> the edges of the bilayer?
If you make the box larger you will have to equilibrate for a long
> danny.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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