Dear Amber people,
I am trying to do minimisation on a 3D model with 3 water molecules and 3 ions
in the active site.
The problem is the total energies of the model with waters and ions could not
reach a stable point. Two sets of runs were tried:
1. 500 iterations run, the total energies keep changing to the 500th run. The
RMS at the end is around 2.95
2. 1000 iterations run, the total energies change in a small range about 10
kcal/mol in the first 500 iterations, but between the 500th and 1000
iterations there is a big drop. Moreover at the end, it still not be to the
stable point. The final RMS is about 1.76 something.
The parameters I used for the minimisation are basic and simple. They are:
&cntrl
imin=1,
maxcyc=1000,
ncyc=500,
ntmin=1,
ntpr=2,
ntr=0,
ntb=0,
cut=12,
&end
I wonder what the realistic standard for the convergence of energy
minimisation and what causes the above things to happen.
Any information is appreciated so much.
Best regards,
Binbin
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Received on Tue Sep 28 2004 - 20:53:01 PDT
