Thanks, Dave. I'll look into this. When you say you have attached
sqm.in, did you mean the e-mail (it wasn't there) or I'll find the
file in the sustiva directory?
Istvan
Quoting case <case.biomaps.rutgers.edu>:
> Hi Istvan:
>
> About minimization methods in sqm, look at the test case in
> amber11/test/antechamber/sustiva. (I've attached the sqm input; you
> can just type 'sqm -i sqm.in -o output-file').
>
> With LBFGS, this input runs for 3650 cycles, reaching a final energy
> of -120.503799 and a gradient of 0.000498. The energy gets to within 0.1
> kcal/mol of its final value after 2270 cycles.
>
> With TCNG, the minimization exits after 10,000 cycles, with a energy of
> -120.3472 and a gradient of 0.001713. It gets to within 0.1 kcal/mol
> of its final energy after 860 cycles, but this is still 0.17 kcal/mol higher
> than the state found by LBFGS.
>
> So: this might be the result of gradients that are slightly wrong,
> or it might
> indicate that one of the parameters defining the TCNG scheme is not set
> correctly in sqm. (Or, something else....)
>
> ...regards...dave
>
>
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Received on Sun Dec 13 2009 - 11:00:03 PST
