[gmx-users] ./mdrun

Roland Schulz roland at utk.edu
Wed Nov 10 03:34:34 CET 2010


as you output says. It infinite long trajectory. Either set a number of
steps (in mdp file or with tpbconf) or set a maximum time with (mdrun -maxh)


On Tue, Nov 9, 2010 at 9:03 PM, lin hen <cuteyy83 at live.com> wrote:

>  Hi,
> I am using the dhfr gpu benchmark with mdrun-gpu:dhfr-solv-RF-2nm.bench.
> export LD_LIBRARY_PATH=/path to OPENMM lib and cuda lib/
> export OPENMM_PLUGIN=/path to OPENMM lib plugins/
> it shows:
> Back Off! I just backed up md.log to ./#md.log.1#
> Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> integrator.
> WARNING: OpenMM supports only Andersen thermostat with the
> md/md-vv/md-vv-avek integrators.
> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
> option.
> Pre-simulation ~15s memtest in progress...done, no errors detected
> starting mdrun 'Protein in water'
> -1 steps, infinite ps.
> and keeps this status for at least one hour, did I miss something? or do
> somthing wrong?
> thanks,
> yy
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