[gmx-users] ./mdrun

lin hen cuteyy83 at live.com
Wed Nov 10 03:03:49 CET 2010

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?
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