From: Aron Broom (broomsday_at_gmail.com)
Date: Sun Aug 19 2012 - 20:03:19 CDT
yeah, looking at the NAMD Energy plugin is probably the simplest. I
suppose that very fact that such a post-processing plugin exists should
have tipped me off to the fact that it isn't something one can simply setup
for a normal NAMD run, as you say.
Thanks,
~Aron
On Fri, Aug 17, 2012 at 4:57 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Aug 17, 2012 at 10:49 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> > Hi,
> >
> > I'd like to pull out the standard energy terms VDW, Elect, etc.. for a
> > selection of atoms during a simulation. I initially thought this should
> be
> > a simple task, but perhaps not? I see there is an NAMD energy plugin for
> > VMD, but this doesn't suit my needs because I'm interested in running
> > Generalized Born implicit solvent calculations, and it doesn't appear to
> > currently support this, so the Born and SASA contributions to the Elect
> > energy would be missing.
>
> what the namdenergy plugin does is simply building custom input,
> then run NAMD and grab the output. if you are a little proficient in
> VMD scripting, it shouldn't be too difficult to either rip out the guts
> of this procedure and make it work for your needs, or - even better -
> add the hooks for what you need in addition.
>
> > I thought there might be a simple Tcl method of scripting this into an
> NAMD
> > run, but I can't figure out how that might be done based on the command
> > options I'm seeing. Is something like this possible at the moment in a
> > simple manner, or would I need to look at either adding it to the NAMD
> > source, or more simply, trying to get the Generalized Born contributions
> > added to the NAMD Energy plugin?
>
> i don't see how this would work in a general NAMD run.
> the Tcl scripting support in NAMD has a very different
> design and purpose as to what VMD does.
>
> axel.
>
> >
> > Thanks,
> >
> > ~Aron
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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