[gmx-users] question about genbox

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Wed Nov 2 01:44:56 CET 2005


> I'm trying to solvate 200 molecules of Glycine in water and I need a 
> certaine concentration in the box. How can I determine the 
> number of water 
> molecules to be added to the glycine. when I run the genbox 
> command it gives 
> me 1712 water molecule and I need them to be 2650 instead.

Couple of options, save a smaller number of waters in a gro file and
tell genbox to add the correct number of those (not sure if it has
improved, but this script use to get some molecules overlapping and with
bad contacts, so take care).  Or adjust the dimensions of the box using
editconf until you get the correct number of water molecules added when
you solvate it.

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 9073
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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