[gmx-users] adding water

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Aug 19 03:50:02 CEST 2003


>thank you for the information, a quick question about it. tbere would be
>no problem with removing the water molecules added by genbox, but how do i
>add the water molecules? and is there any way to control how many are
>added? thanks again.

With genbox you can specify now many molecules are added using the "-nmol" 
switch, and don't use "-cs", but "-ci" for the water molecule  But they 
will be spread throughout the entire box, except where other molecules are 
located.  So you probably have to add more than you actually want in there, 
depending on the ratio in the box volume above and below the monolayer i.e. 
if it was dead center then adding double the number of water molecules 
should approximately put the right number below it.

Or, you would need to write a script that adds them yourself.  I haven't 
done this myself, but a colleague here has written one that inserts 
molecules randomly into a given box (the random molecule engine with genbox 
has some problems).  Wouldn't be too much of an issue to add constraints on 
the region within the box to place them  You would just have to specify the 
coordinate file to insert them into, the coordinate file for the water 
molecule, how many to insert, and the allowable regions of the box i.e. 
where the "bottom" of the monolayer is located.  How you do this code wise, 
well, best idea I suppose is look at the coding for genbox.

Hope this helps.

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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