[gmx-users] Visualization Problem

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Tue May 8 05:17:35 CEST 2007

Probably means that atoms are moving across the pbc boundary from one
side of the box to another.  The visualiser you are using is trying to
maintain the bond between the atoms after the move, so draws it all the
way across the box itself.  Two ways to fix, don't visualise the bonds,
using either points or ball representations for the atoms, or when
generating the trajectory do so that atoms don't go jump across the box

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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