[gmx-users] genbox

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Feb 12 00:37:19 CET 2003

According to the documentation, genbox:

"3) Insert a number (-nmol) of extra molecules (-ci) at random positions. 
The program iterates until nmol molecules have been inserted in the box. To 
test whether an insertion is successful the same VanderWaals criterium is 
used as for removal of solvent molecules. When no appropriately sized holes 
(holes that can hold an extra molecule) are available the program tries for 
-nmol * -try times before giving up. Increase -try if you have several 
small holes to fill"

Are these features actually implemented in 3.1.4?

Reason I ask is while inserting multiple molecules into a box, some end up 
practically on top of each other and are impossible to em.  And when you 
are inserting a lot of molecules into a box, with long chains, it can take 
some time to find a box version that is suitable to use.

Catch ya,

Dr. Dallas Warren
Research Fellow
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 9076
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