Hello Charles,
Thanks. That makes sense and it works. :-)
Good day,
Santhosh
On Tue, Aug 27, 2013 at 12:15 PM, Charles Schwieters <char...@schwieters.org
> wrote:
>
> Hello Santhos--
>
> >
> > I was able to successfully load the pdb files using both loadPDB and
> > initCoords [i generated a psf file using pdb2psf and since the psf would
> be
> > the same for all the ensemble simulation members I think thats OK].
> >
> > But I am not really sure if its doing the right thing. Just to be clear
> of
> > the question:
> > I want different ensemble members to have different starting structures.
> > Here is the snippet of the code, my reason for confusion in comments :
> >
> > protocol.initRandomSeed()
> > protocol.initParams("protein")
> > ensembleSize = 2
> > pdbFiles = ["model0.pdb","model1.pdb"] # these two files should be the
> > starting structures
> >
> > esim = EnsembleSimulation("ensemble",ensembleSize)
> > memberIndex = esim.member().memberIndex() # this makes memberIndex = 0
> > protocol.initStruct('model.psf') # the default psf file
> > protocol.initCoords(pdbFiles) #
>
> close: please instead use
>
> protocol.initCoords( pdbFiles[memberIndex%2] )
>
> >
> > The same code as Charles has wrote :
> > protocol.initCoords(pdbFiles[memberIndex%2]) # using 2 structures,
> > memberIndex%2 would always be zero as memberIndex =0, means the code
> loads
> > only one file.
>
> No. memberIndex is 0 or 1 for a 2-membered ensemble. To better see
> what is going on, you can enable output for those having non-zero
> memberIndex by adding the flag
>
> -thread_filename thread.out
>
> to the xplor command invocation. You will then have files for each
> non-zero ensemble member ion your directory.
>
> best regards--
> Charles
>
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