From: John Stone (
Date: Thu Jan 14 2016 - 15:36:04 CST

  Please CC VMD-L on replies so that others can read and learn from
resolutions from questions like yours.

There are a number of existing plotting scripts and plugins that will
do the kinds of display that you seem to be looking for. Here are several
worth evaluating that are already built-into VMD:

I know of a few custom plotting scripts people have written that
have the same sort of interactive selection and linkage to the
trajectory like ramaplot does, but I don't think they are posted
on the web at this moment. Have a look at the items above
and see if those look like something you could work with or modify
to do what you want.

  John Stone

On Thu, Jan 14, 2016 at 05:38:28PM +0100, Matthias Ernst wrote:
> Hi John,
> I was mainly thinking about energy landscapes for a (long) MD
> simulation, as e.g. generated by PCA.
> Usually, we use 1D or 2D projections and it would be really nice if
> these could be shown in a similar way like the Ramachandran plot
> analysis tool does.
> Another 1D example would be energy during an energy minimization (good
> old molden does it nicely for QM simulations) or temperature. pressure,
> radius of guration,... during an MD or similar data, where it would be
> instructive to see both the structure and the data point in the
> corresponding curve at the same time.
> Should I provide some sample input for my examples?
> Thanks,
> Matthias
> On 01/13/2016 07:05 PM, John Stone wrote:
> > Hi,
> > With a little bit of scripting, it is certainly possible to
> > load arbitrary 1-D or 2-D data and associate it with MD trajectory
> > frames and have the two linked in various ways. Do you have a
> > particular example of the sort of information that you're interested
> > in loading and interacting with?
> >
> > Cheers,
> > John Stone
> >
> >
> > On Fri, Jan 08, 2016 at 07:55:49PM +0100, Matthias Ernst wrote:
> >> Hi,
> >>
> >> first of all, thanks for the nice software VMD which I really enjoy
> >> working with!
> >>
> >> I have a question. When I load an MD trajectory of a protein and
> >> calculate the Ramachandran plot, I can scroll through the trajectory and
> >> the current value in x/y is automatically shown in the plot. On the
> >> other hand, if I click on a point, the corresponding frame is chosen.
> >>
> >> Is it also possible to load external data (in 1D or 2D) and show it in
> >> the same way (highlighted when scrolling, possibly even going to the
> >> timeframe when selecting)?
> >>
> >> Thank you very much,
> >> Matthias Ernst
> >>
> >> --
> >> Progress...
> >
> --
> Progress...

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