Hi, Charles,
Thanks! It is clear to me now.
Another question: in order.py, the force constant of ANGL and IMPR are
ramped by
MultRamp(ini_ang,fin_ang,"potList['ANGL'].setScale(VALUE)")
MultRamp(ini_imp,fin_imp,"potList['IMPR'].setScale(VALUE)")
How do these set values (k_ang and k_imp?) work in the calculation?
In the old fashion, it looks like:
command("""
constraints
inter = (resid 1:76) (resid 1:76)
weights * 1 angl %f impr %f vdw %f end
end""" % ( k_ang, k_imp, scaleVdw) )
Does it do the same thing in order.py?
Thank you very much!
Best wishes,
Jie-rong
2008/11/12 <Charles at schwieters.org>
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> Hello Jie-rong--
> >
> > Thanks for your suggestion. I tried to understand this order.py
> > script from gb3_ensemble, but there are still some parts that still
> > confused me.
> >
> > The biggest difference I can tell between the script I posted in previous
> > e-mail and order.py is that there is a Powell minimization following the
> > dynamics at each temperature during the cooling steps. Is this the
> feature
> > that you suggested "can't mix EnsembleSimulaition with XPLOR
> minimization"?
> > I don't understand this. Could you explain more? Or some reference
> > suggested to read?
>
> The biggest problem with your script is the direct calling of the XPLOR
> mini powell statement. This will not work with EnsembleSimulations. The
> use of DynMin in order.py is probably not necessary.
>
> >
> > You also mentioned "the scaling of energy results in a time scaling, such
> > that larger ensembles should use longer times for dynamics". Does it
> mean
> > that if larger ensemble size is used, the dynamics time should set longer
> > manually (for example, set finalTime 1 ps to 10 ps )? Or does it mean
> the
> > "delta_t" between dynamic steps become shorter when the size of ensemble
> is
> > larger, and it takes longer (more computer time, more steps) to reach
> > finalTime?
>
> You may need to manually set finalTime to be a larger value. Please try
> without doing this first, though.
>
> >
> > In addition, any difference between potList.add, and potList.append,
> since
> > both are used in order.py? Thanks a lot!!
> >
>
> There is no difference. potList.append is now preferred, as this is the
> name of the method used by native Python lists.
>
> best regards--
> Charles
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