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

Live King vikasdubey1008 at gmail.com
Mon Dec 21 07:38:44 CET 2015

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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