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

Mark Abraham mark.abraham at anu.edu.au
Thu Mar 8 12:27:01 CET 2007

> 8 mar 2007 kl. 01.32 skrev Mark Abraham:
>>> 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
>> around.
>> Mark
> I'm not so sure about that. genbox *does* take a top file as an
> optional argument. genbox -h tells me:
> "Finally, genbox will optionally remove lines from your topology file
> in which
> a number of solvent molecules is already added, and adds a line with the
> total number of solvent molecules in your coordinate file."
> I have never used this option, so I don't know exactly how it works,
> but I expect it to do what William wants it to do.

Maybe this works, I've never used it either... but the point is that the
source of the information about how many waters to add comes from the
genbox command line, not this .top file. I think William wanted the number
of waters in his .top file to be added to his .gro file, and this is an
ill-defined proposition.


More information about the gromacs.org_gmx-users mailing list