Dear Amber Community,
I'm successfully running a simulated annealing protocol using sander for a
small ligand.
In order to find the global minimum I have to heat and cool the system
several times.
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?
Thank you very much for your answers.
Kind Regards, Julian
The protocol is the following:
Simulated Annealing Protocol
&cntrl
imin=0,nmropt=1,dielc=80.,
ntpr=50,ntwr=500,ntwx=0,
ntb=0,cut=20,vlimit=10,
ntt=3,gamma_ln=1000,nstlim=500000,dt=0.001,
pencut=-0.001,offset=0.09,
/
&wt type='TEMP0', istep1=0,istep2=70000,
value1=0., value2=5000., /
( ... )
&wt type='END' /
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Received on Tue Sep 13 2011 - 07:30:05 PDT
