Hi,<div><br></div><div>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)</div><div><br></div><div>Roland<br><br><div class="gmail_quote">
On Tue, Nov 9, 2010 at 9:03 PM, lin hen <span dir="ltr"><<a href="mailto:cuteyy83@live.com">cuteyy83@live.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
Hi,<br> <br>I am using the dhfr gpu benchmark with mdrun-gpu:dhfr-solv-RF-2nm.bench.<br>
export LD_LIBRARY_PATH=/path to OPENMM lib and cuda lib/<br>
export OPENMM_PLUGIN=/path to OPENMM lib plugins/<br>
it shows:<br>
Back Off! I just backed up md.log to ./#md.log.1#<br>Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)<br>
Back Off! I just backed up ener.edr to ./#ener.edr.1#<br>
WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator.<br>
<br>WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators.<br>
<br>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.<br>
<br>Pre-simulation ~15s memtest in progress...done, no errors detected<br>starting mdrun 'Protein in water'<br>-1 steps, infinite ps.<br><br>
<br>
and keeps this status for at least one hour, did I miss something? or do somthing wrong?<br>
<br>
thanks,<br>
<br>
yy<br> </div>
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