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Hello Marco--
>
> In def calcOneStructure(loopInfo): (line numer 267) there is following part
> defined:
>
> # optional cooling in Cartesian coordinates
> #
> protocol.initDynamics(minc,
> potList=potList,
> numSteps=100, # at each temp: 100 steps or
> finalTime=.4 , # .2ps, whichever is less
> printInterval=100)
> #cart_cool.run()
>
you are correct. For that optional calculation to work you need the
following statement first:
cart_cool = AnnealIVM(initTemp =init_t,
finalTemp=25,
tempStep =12.5,
ivm=minc,
rampedParams = rampedParams)
I've fixed up gb1_rdc/anneal.py for future releases.
thanks--
Charles
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