[gmx-users] GPU - protein in water

Steven Neumann s.neumann08 at gmail.com
Thu Aug 9 09:49:28 CEST 2012

Dear Gmx Users,

I have on the HPC cluster installed  Gromacs VERSION
4.6-GPU-dev-20120607-7ce3372 (called gromacs 4.6-hybrid-beta). I want
to simulate chain of 80 residues in explicit solvent model using GPUs.

Has anyone simulated the system like this under this version and can
advise about mdp options? I know I have to use Amber or Charmm
(-nocmap), Andersen thermostat, pbc=xyz. Any other requirements?

Can I use tpr file for mdrun produced by Gromacs 4.5.4?

Thank you,


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