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Hello Bryn--
> >
> >>
> >> I would like to have two separate parts of the shape term or two
> >> separate RMSD terms for two independent domains. Can you suggest some
> >> syntax for this?
> >>
> >> I have a single replica simulation and would like to use the shapePot
> >> term.
> >>
> >> The problem is that I am a little confused regarding the syntax.
> >>
> >> ...
> >>
> >> I presume that a block like this should work, but how can I specifiy
> >> that I want the shape restrained to that of the starting structure?
> >>
> >
> > Let me first understand exactly what you're looking to do: do you wish
> > to perform a structure determination holding domain positions rigid? If
> > so, it would probably be best to just group domain atoms into regidi
> > regions using the IVM's group method. Something like:
> > dyn.group('sel for domain 1')
> > dyn.group('sel for domain 2')
> >
> > You can omit sidechains if you wish to allow them to move. Is this close
> > to what you want, or is it something else?
> >
> Yes this is just a structure calculation. As long as I can keep the
> two domains as rigid as possible while at the same time letting them
> move relative to one another your suggestion will fix my problems.
Then IVM grouping will do what you wish. Please let me know if you have
problems with this.
best regards--
Charles
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