[gmx-users] Multiple "Random" Molecule Placement

Dallas Warren dallas.warren at vcp.monash.edu.au
Mon Sep 23 03:00:23 CEST 2002

Using genbox to insert multiple molecules into the box, I have found that 
it tends to place a couple such that they are very close together, if not 
intertwined.  Will increasing the -vdwd value help to avoid this problem?

Additionally, I have found that using genion it is far better to use the 
-random switch in the placement of larger concentration of back ground 
salt, rather than placement based on potential.  Otherwise it performs some 
rather unusual placement of the ions, i.e., in a grind along one face of 
the box after it has placed some throughout the box.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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