On Sat, Apr 01, 2017, danil kutov wrote:
>
> 1.Optimization with gradient methods (ntmin = 0-2). The protein is rigid
> and coordinates of all ligand atoms are varied. The optimization does
> not stop at the minimum configuration!
I don't understand what you mean here, and missing details make it harder.
What tolerance criteria are you asking for (drms, maxcyc)? Does the
calculation reach that tolerance yet not stop? Given that you will certainly
not find a minimum for the solvated surface, are you perhaps asking for too
tight a convergence?
>
> 2.It is possible to use the XMIN (ntmin = 3) method or the LBFGS method
> (xmin_method = 'LBFGS') but the optimization is finished after several
> first steps with ERROR in load_lbfgs(): YS=0. How is it possible to
> avoid this error?
Use method = 'TCNG'. Note that the xmin methods can have problems when
the energy surface is not continuous, as when one is using nonbonded cutoffs.
I don't know of any good way to simultaneously have a smooth energy surface
and a very fast calculation.
....dac
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Received on Sat Apr 01 2017 - 06:30:02 PDT
