VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Apr 14 2008 - 10:24:53 CDT

Hi Irene,
could you give an example of what you've tried and what happens?
Peter

Irene Newhouse wrote:
> I've written a script, but I'm having trouble figuring out how to
> deploy it in command line, text mode, of all things. No matter
> what I try, the system claims 'bigdcd' is an invalid command - even
> when I add the full path to bigdcd, explicitly.
>
> Thanks!
> Irene
>
> ------------------------------------------------------------------------
> From: einew_at_hotmail.com
> To: petefred_at_ks.uiuc.edu
> CC: vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: Using namdenergy in batch mode to compute
> dihedral energies
> Date: Thu, 10 Apr 2008 16:17:08 -1000
>
> Thank you!
>
> Irene
>
> > Date: Thu, 10 Apr 2008 17:05:18 -0500
> > From: petefred_at_ks.uiuc.edu
> > To: einew_at_hotmail.com
> > CC: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: Using namdenergy in batch mode to compute
> dihedral energies
> >
> > Hi Irene,
> > if you run namd with one pairInteraction group instead of two,
> you'll
> > end up getting internal energies (including dihedrals), which
> you should
> > then be able to parse to pull out the dihedral energy. Please
> note that
> > pairInteractions may behave in slightly unintuitive ways if you are
> > calculating bonded interactions for only a subset of a segment; for
> > example, if you have a set of bonded atoms 1-2-3 and you use
> atoms 1 and
> > 2 in the pair interaction group, you will end up getting
> energies for
> > both the 1-2 and 2-3 bonds. Similar logic extends to dihedrals.
> If you
> > want to have more fine grained control to measure a single dihedral
> > (rather than a dihedral energy for a chunk of your structure)
> you may
> > instead want to use vmd's measure energy command with bigdcd.
> > Best,
> > Peter
> >
> > Irene Newhouse wrote:
> > > Using the sample config file at
> > > http://www.ks.uiuc.edu/Research/namd/2.6/ug/node42.html I've
> been able
> > > to compute interaction energies
> > > for a trajectory in batch mode. I'd like to do the analogous
> thing for
> > > dihedral energies of certain parts of my structure, but I'm
> not sure
> > > how to modify the sample config file appropriately - what do I
> use in
> > > place of the pairIneraction lines? I don't want to call the
> namdenergy
> > > plugin through VMD because my trajectories are too long to
> load into
> > > VMD - not enough memory per node.
> > >
> > > Thanks!
> > > Irene Newhouse
> > >
> > >
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