[gmx-users] topol inaccessible in the production md step

Justin Lemkul jalemkul at vt.edu
Wed Jul 25 14:16:36 CEST 2018

On 7/25/18 7:24 AM, Raag Saluja wrote:
> Hi!
> I'm simulating a heterodimer, with the help of your lysoyme tutorial. The
> simulation runs smoothly till the production MD step.
> I gave these commands:
> gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
> time -p mpirun gmx_mpi mdrun -v -deffnm md
> I kept md.mdp identical to the one given in the tutorial, except that I
> changed the number of steps to 25000000.
> I got an error saying that 'topol' was inaccessible or didn't exist. The
> topol file is very much there and all the previous commands worked. Where
> am I going wrong?

Your naming is inconsistent. You made a .tpr file called "md_0_1.tpr" 
and then you're asking mdrun to execute "md.tpr," which does not exist. 
Since mdrun cannot find "md.tpr," it looks for the default file name, 
"topol.tpr," which it also doesn't find. Hence, you get a fatal error.



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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