[gmx-users] benchmarks

Justin Lemkul jalemkul at vt.edu
Tue Jul 3 17:57:30 CEST 2018

On 7/3/18 11:53 AM, Mahmood wrote:
>> You don't need a PDB file for anything if you have conf.gro. With
>> topol.tpr, you also don't need to regenerate any .tpr file, unless
>> you're trying to compare with a different version, but you can generate
>> a topology from conf.gro and use the provided .mdp file to create a new >.tpr file.
> Similar to the Lysozyme tutorial, I ran the following command
> gmx grompp -f grompp.mdp -c conf.gro -p topol.top -o file.tpr
> The error is
> ERROR 1 [file grompp.mdp]:
>    With Verlet lists rcoulomb!=rvdw is not supported (except for
>    rcoulomb>rvdw with PME electrostatics)

As with the tutorial problems you posted, you're using inputs designed 
for an old version of the software (5.0, as stated on the benchmark 
website) and trying to use them in a newer version that has different 
requirements. The benchmarks were run with 5.0 and that's what you 
should assume works. If you want to use 2018, you need to update the 
inputs appropriately.



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


More information about the gromacs.org_gmx-users mailing list