[gmx-users] Problem with mdrun and shell particles (polarizable ff)

[Justin Lemkul]

On 9/13/18 7:56 AM, Matteo Busato wrote:
> Hi to everyone,
>
>
> I am trying to perform a calculation on a cluster, where Gromacs 5.1.4 was compiled, using a polarizable force field carrying shells. Since domain decomposition can not be used, I was trying to launch mdrun with  the -ntmpi 1 -ntomp=number-of-cores options as Justin stated in an old discussion (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-September/092341.html). However, the program gives me this error:
>
>
> Fatal error: "Setting the number of thread-MPI ranks is only supported with thread-MPI and GROMACS was compiled without thread-MPI".
>
>
> Since I have not the superuser permission for this cluster, is there any solution that avoids recompiling Gromacs?

GROMACS needs to be compiled with thread-MPI support, and you can always 
install your own version of the code within your home directory without 
needing su.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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