Hi Till--
>
> > 2) Do the calcXTensor procedure separately, as you are doing now, but
> > then restrain the positions to be the same during the remainder of the
> > calculation. This may be better, since there is no reason the
> > alignment tensors will be the same.
>
> As of now, all PCS sets are based on the same (in-silico) Terbium atom.
> So that should already do the trick?
Indeed- this is what I intended.
>
> > This indicates a problem with the IVM setup. I *might* be able to figure
> > out the problem if you send the complete script.
>
> I created and attached an archive, with which I can reproduce the
> behaviour. It also includes some needed modifications. Hopefully there
> is no problem running this, otherwise I could try sending it
> differently.
I received your .zip file successfully, but I suggest that you send
such information directly to my email, as this is a public mailing
list.
I ran the script run.py successfully. One thing which bothers me, is
that you seem to be using an intermediate release of Xplor-NIH. I
suggest you try the current release, version 3.2.
A few things:
1) Currently, the alignment tensor Da and Rh are fixed at the values
from the initial calls to calcXTensor. You might add the bits from
eginput/fold.py in the Xplor-NIH distribution I included below to
optimize these parameters during final minimization. The calls to
setFreedom should be done before the calls to protocol.torsionTopology
or protocol.cartesianTopolgy. The file eginput/refine.py takes a more
aggressive approach to tensor parameter optimization allowing Da and
Rh to float throughout, using calcTensor at each simulated annealing
temperature.
2) You might wish to increase the PCS fore constant.
3) The script runs somewhat slowly due to the PyPot term you
wrote. Addressing bottlenecks in that term will make the calculation
faster, but this you probably understand well.
The crash you reported looks like a problem with the IVM setup of
pseudoatom topology.
dyn.addConfigAction( IVMAction("""
for m in media.values():
m.setFreedom("fixDa, fixRh") #fix tensor Rh, Da, vary orientation
""") )
minc.addConfigAction( IVMAction("""
for m in media.values():
m.setFreedom("varyDa, varyRh") #vary tensor Rh, Da, vary orientation
""") )
########################################################################
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