Hey Jiom,
I've had the exact same issue trying to run benchmark systems on GROMACS
vs. AMBER a few weeks ago. I have found that I can limit the number of
solvent molecules using genbox (with -maxsol) from Gromacs. Assuming Amber
was closer to correct density, I have instructed Gromacs to introduce as
many water molecules as Amber does.
I don't know the actual reason behind the issue but this protocol worked
fine for me. Even though the Gromacs box was half empty in the beginning it
quickly equilibrated and ran without errors.
Regards,
Murat
On Fri, Jun 13, 2014 at 4:04 PM, 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?
>
> Thanks
> jiom
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Received on Sat Jun 14 2014 - 16:30:02 PDT
