[gmx-users] Free Energy calculations with GROMACS 5.0.5 on cluster

[Mark Abraham]

Hi,

If you're running GROMACS compiled with MPI support, then your command line
should start e.g. mpirun -np gmx mdrun. Consult your cluster documentation
for details.

Mark

On Mon, 21 Dec 2015 16:39 Live King <vikasdubey1008 at gmail.com> wrote:

> Hi everyone,
>
> I am running free energy calculations on my cluster using GROMACS 5.0.5. I
> have 21 windows so, I run my simulations parallely. I am fairly new to
> GROMACS 5.0.5 and had used version 4.5.5 before. In that case I used "-np
> 2" or "-np 1 " option of mdrun to run parallel simulations.  GROMACS 5.0.5
> doesn't seem to recognize -np option. I tried -nt 1 and  -nt  2 then It
> gives this error.
>
>
>
>
>
> *Fatal error:Setting the total number of threads is only supported with
> thread-MPI and Gromacs was compiled without thread-MPI*
> so, I tried removing both options and now whenever I run my simulations on
> cluster they are really really slow. Is this a problem of GROMACS
> installation ?
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