Hi Guillermo,
Potentials should be added to the IVM via the Python or TCL
interfaces. The 'classic' flags statement exists for backwards
compatibility.
Unfortunately, it uses a rather low-level mechanism that's
incompatible with (and doesn't know anything about) any
of the new potentials written using the new interfaces.
--JK
On Sep 26, 2005, at 5:00 PM, guillermo bermejo wrote:
> Dear all,
>
> When writing a python script you can add old xplor commands by running
> xplor.command('<xplor-command>'). As a result, there are tasks that
> can be
> performed redundantly in both the xplor and Python languages:
>
> >seed = 322111
> >xplor.command('set seed = i% end' % seed) # this...
> >simWorld.setRandomSeed(seed) # is
> equivalent to this.
>
> However, I've noticed that for certain other tasks the xplor and
> Python
> interfaces are invisible to each other. For example,
>
> >from ivm import IVM
> >dyn = IVM()
> ># set up topology here (fix, group, etc.)
> >dyn.autoTorsion()
> >
> ># The flags include xplor command doesn't work.
> >#command('flags exclude * include bonds angle impr vdw rama end')
> >dyn.potList().removeAll()
> >dyn.potList().add( XplorPot('BOND') )
> >dyn.potList().add( XplorPot('ANGL') )
> >dyn.potList().add( XplorPot('IMPR') )
> >dyn.potList().add( XplorPot('VDW') )
> >dyn.potList().add( XplorPot('RAMA') )
> >
> ># set up dynamics parameters here.
> >dyn.run()
>
> In the above piece of script, setting the active energy terms using
> the
> xplor "flags include" statement has no effect (and the dynamics
> would run
> using the terms turned on by default). In this case, the xplor
> commands are
> "invisible" in the python interface.
>
> Is there a clear distinction between tasks that can be performed
> equally by
> both interfaces (like setting the seed number), and others that
> should be
> performed by either using the xplor commands or the python
> interface, but
> not a mixture of both?
>
> Thanks in advance. Best regards,
>
> Guillermo Bermejo
> PhD candidate
> Chemistry Dept.
> Carnegie Mellon University
> Pittsburgh, Pa.
>
>
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>
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