[gmx-users] problem with genbox

Dallas Warren dallas.warren at vcp.monash.edu.au
Thu Aug 19 01:48:55 CEST 2004

>The resulting output contains atoms which are too close. The distance 
>between the atoms is sometimes
>as small as 0.01 nm which is smaller than the vanderwaals radii from the 
>database vdwradii.dat . Not
>surprisingly, therefore I get errors when I run energy minimization or mdrun.
>  The output keeps repeating the message "tested 0 pairs,  removed 0 atoms 
> " as I quote below.  I would
>greatly appreciate if somebody could guide me how to use genbox properly.

genbox isn't that good at randomly placing molecules within a box in cases 
like this (are some emails in the archive on this).  It needs a bit of 
work.  I use an in house program to do it, works out much better.  Although 
I don't have it to give out to anyone, since it is part of a much larger 
package that does a lot of other things and isn't mine to make available.

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 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.

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