zen...@graduate.org skrev 2011-03-22 10.22:
when i type this order :szrun 2 2 mdrun_mpi -nice 0 -v -s pr.tpr -o
pr.trr -c b4md.pdb -g pr.log -e pr.edr &
the process can not run,and there is a problem that t = 0.000
ps: Water molecule starting at atom 90777 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates.
i have made the dt =0.001and nsteps=10000 in the em.mdp ,but the order
(szrun 2 2 mdrun_mpi -nice 0 -v -s pr.tpr -o pr.trr -c b4md.pdb -g
pr.log -e pr.edr & ) still can not run .how to slove this problem ?
Changing timestep won't help. Your simulation crashes at t=0.0, which
means your system isn't properly equillibrated, or there are errors in
the topology.
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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