[gmx-users] genbox give coord file more waters than top file

Mark Abraham mark.abraham at anu.edu.au
Thu Mar 8 01:32:29 CET 2007

> Dear gromacs guys
> Why would genbox put more water molecules in my .gro file than in my .top
> file? I'm sure all I have to do is edit the number in my top file, but I
> have not had this happen before, does anyone know of  a reason that this
> happens so I can fix my file?

genbox doesn't read a top and produce that many solvent molecules. For a
start, how does it know what shape you want them in? Read "man genbox",
choose what you want to do, apply genbox, and then edit your .top so the
number of waters agrees with what genbox produced... not the other way


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