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

Justin Lemkul jalemkul at vt.edu
Thu Sep 13 14:13:28 CEST 2018

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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