Re: [AMBER] different number of waters

From: Jason Swails <>
Date: Sun, 15 Jun 2014 01:07:41 -0400

On Fri, Jun 13, 2014 at 9:04 AM, newamber list <>

> Hi All
> I am solvating same system with truncated octahedron box and want to run
> with both AMBER and GROMACs. In AMBER, am using 12 Ang buffer with
> solvateoct and get around 76716 water molecules but with Gromacs with same
> buffer I am getting around 132902 waters (almost twice). These are
> following commands am using:
> with AMBER:
> solvateoct sol TIP3PBOX 12
> with GROMACS:
> editconf -f input.gro -o output.gro -c -d 1.2 -bt octahedron
> I am not sure whats wrong, please let me know if someone got similar
> issues?

​I'm not familiar with Gromacs at all. However, you can always experiment
with Amber and keep making the buffer size a little larger until you get
_almost_ the number of water molecules you want, plus a small number more.

Then you can use ParmEd or cpptraj to create a new topology file by
stripping away the "extra" water molecules.

In order for GROMACS and Amber to be getting that big of a difference in
the total number of solvent molecules, they must be doing different things.
 Since I don't know any specifics about gromacs, I don't know how to
specifically help.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Jun 14 2014 - 22:30:02 PDT
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