[gmx-users] benchmarks

Justin Lemkul jalemkul at vt.edu
Tue Jul 3 15:27:09 CEST 2018

On 7/3/18 9:13 AM, Mahmood wrote:
> Hi,The benchmark package [1] has no readme on how to run the benchmarks. In each folder I see conf.gro, *.mdp and topol.tpr.
> Following the tutorials, there is no pdb file there. I need that to build tpr file and that is used in gmx mdrun. Can someone shed a light on that? Where could I find more information?

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.



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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