[gmx-users] Re: grompp error

Dr. Vitaly Chaban vvchaban at gmail.com
Tue Oct 23 12:10:11 CEST 2012

> Luckily ialready found my error..
> I need to find the gro file spc216.gro and pack it with my co-solvent
> After that i run it in minimization part by using the command
> grompp -f em1.mdp -c pacl.gro -p topol.top -o minimize.tpr -v
> mdrun -deffnm minimize -v
> Need to edit the em1.mdp by using the highest emtol starting from 1000
>  and decrease it little by little to get the lowest energy.

You should not "decrease it little by little", but simply specify the
force threshold, which you need for your system. If you intend to run
dynamics afterwards, the threshold of 1000 provides a viable setup.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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