On Fri, Jun 13, 2014 at 9:04 AM, newamber list <newamberlist.gmail.com>
wrote:
> 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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 14 2014 - 22:30:02 PDT
