From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Mon Jul 05 2004 - 09:46:24 CDT
Yes, you can use "measure minmax" in VMD to get the box dimensions. You should preferably use cell basis vectors a little larger than the the numbers you get from the "measure minmax" command, to prevent 'clashes' between water molecules between your simulation system and the images (although minimization might solve these). See also the example of the config-file with periodic boundary conditions from the tutorial files (ubq_wb_eq.conf and p.20 in the tutorial).
good luck,
Marc
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of Raymond C. Fort Jr.
Sent: Mon 5-7-2004 14:57
To: namd-l_at_ks.uiuc.edu
Cc:
Subject: namd-l: Cell Basis Vectors
How does one determine the cell basis vectors when setting up a simulation
in a periodic box? I have used the "measure minmax" command to obtain the
dimensions of the box. Am I correct to assume that these are the numbers I
need?
Thanks for any help!
Ray
Professor Ray Fort Jr. rcfort_at_maine.edu
Department of Chemistry chemistry.umeche.maine.edu/fort.html
University of Maine Voice: (207)-581-1180
Orono, ME 04469 FAX: (207)-581-1191
Computer modeling of organic and biomolecules; chemistry of lignin
and cellulose
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