[gmx-users] mdrun the pr.trr

[Erik Marklund]

zengyq at 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.

-- 
-----------------------------------------------
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
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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