From: Matthias Ernst (
Date: Thu Jan 14 2016 - 10:38:28 CST

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?


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...