Hi,
> As I see it, the output I get is always the last snapshot which is not
> necessarily the one with the lowest energy.
> Is this true? And how can I change this, how do I get the lowest energy
> snapshot of my simulation?
Amber will write a restart at the end of the simulation only. If you want
intermediate snapshots, you would normally set
> The protocol is the following:
>
> Simulated Annealing Protocol
> &cntrl
> imin=0,nmropt=1,dielc=80.,
> ntpr=50,ntwr=500,ntwx=0,
^^^^
ntwx to some value, e.g. 50 to get energies and trajectory frames every 50
steps as the mdcrd file. If you want a restart file for each snapshot
instead, check the manual entry for ntwr (the <0 option).
Kind Regards,
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Sep 13 2011 - 07:30:08 PDT
