[gmx-users] implicit water simulation mpi

[Mark Abraham]

Hi,

The last version where implicit solvent was known to work in parallel was
4.5.7 unfortunately. It wasn't maintained since then, and has been removed
in very recent versions. Either use 4.5.7 or some other software, e.g.
AMBER.

Mark

On Sun, 12 May 2019 at 01:33, Halima Mouhib <fatim_1998 at yahoo.com> wrote:

> Hi,
> I have a question on how to run implicit water simulations using the
> Gromacs5.x series.
> Unfortunately, there is a problem with the domain decomposition when using
> the command:  gmx mdrun -deffnm md -v
>
> #################
> Fatal error:
> Domain decomposition does not support simple neighbor searching, use grid
> searching or run with one MPI rank
> #################
>
> and it works fine with one MPI rank ( gmx mdrun -deffnm md -v -nt 1 ), but
> I need it to run in parallel otherwise it is too slow.
>
> In the previous Gromacs4.x versions, this could simply be solved using the
> point decomposition method (mdrun -pd).
>
>   How this has been replaced in Gromacs5.x?
>
> Thanks a lot in advance!Lima
>
>
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