VMD-L Mailing List

From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Wed May 08 2002 - 11:01:26 CDT

Hi Mark,

On Wed, May 08, 2002 at 08:58:28AM -0400, Storr, Mark wrote:

> thanks for replying to my mail, what you sent is what I had in my mind from
> the description as I cannot get the demo to work due to the following error:
>
> Opened sensor config file C:.........vmdsensors
> expected integer but got ""Not valid molecule id in atomselect's 'moilid'

        Ah, I see that version used a recently-added scripting
feature. I've attached a new version that works with vmd 1.7.1 and
above (and possibly earlier versions). Same instructions as in my
previous email.

>
> I was hoping that somehow one would be able to read the output file from a
> NAMD simulation and plot the variables saved in the file along with
> animation.
  
    The attached script gives you the "animating" part of "animating
MD trajectory energy profiles" -- with the user left with the task of
plugging in her analysis results, as you surmised. Fortunately, the
"energy profiles" part has actually been under active devleopement
over the past couple of weeks. New versions of NAMD with more energy
analysis features, and scripts which combine NAMD and VMD to do just
what you have in mind, could be released soon, perhaps even in the
next few weeks. I'll make sure that vmd-l is told about any
developments here.

        
                                Cheers,

                                Barry

>
>
>
> -----Original Message-----
> From: Barry Isralewitz [mailto:barryi_at_ks.uiuc.edu]
> Sent: Tuesday, May 07, 2002 11:15 PM
> To: Storr, Mark
> Cc: vmd_at_ks.uiuc.edu
> Subject: Re: Animating Trajectories/NAMD Output files
>
>
> Hello,
>
> On Tue, May 07, 2002 at 02:06:43PM -0400, Storr, Mark wrote:
> > Hi,
> >
> > I was wondering if it is possible to animate an MD trajectory from NAMD
> and
> > to also have displayed in a number of graph windows the total energy/vdws
> > etc. profiles displayed from the output file for the simulation so that
> one
> > could follow/pause the animation at 'energetically' interesting points.
> > If anyone has done this I would be grateful for any help with this matter,
> > or if not may I suggest it as a possible addition to future versions of
> VMD.
> >
> > Many Thanks
> >
> > Mark
> >
> > Mark T. Storr
> > Postdoctoral Fellow
> > Steacie Institute for Molecular Sciences
> > National Research Council
>
>
> We have a few tools in the works for this.
>
> 1.) Line graph: (value) vs. (trajectory frame) graph.
>
> 2.) Surface graph: (value) vs. (resiude) vs. (trajectory frame).
>
>
> For both graph types a marker follows the current frame (i.e. moves
> when trajectory is animating) and can be clicked on or "scrubbed" over
> the graph, changing the displayed trajectory frame.
>
> I have attached a rough version of type 1), a line graph. It
> needs some hand-tuning for each data set (see instructions). The file
> includes a demo (that makes its own trivial trajectory). Copied below are
> the comments/instructions that appear at the start of the file. Multiple
> graphs
> can be set up with multiple tcl 'trace' commands. Let me know if this
> is the sort of thing you had in mind...
>
> Cheers,
>
> Barry
>
> # graph-drag.tcl
> #
> # Show a graph with value based on vmd frame number.
> # Clicks and drags in graph window move trajectory.
> #
> # To demo:
> # 1. vmd -e graph-drag.tcl
> # 2. demo_graph_drag
> # (makes a trajectory of a rotating molecule
> # and a sample data set)
> # 3. In "Animate" window, click 'Forward' button.
> # 4. Click and drag on graph window to move in trajectory.
> #
> # To use:
> # 1. replace "make_data" proc with one that puts useful data in y_cache
> # 2. Adjust "mult" and y-scale labels to fit your data set.
> # 3. Run with: make_data, start_graph
> #
> # Still needs: auto-scaling, reasonable interface, etc.
> #
> # Barry Isralewitz May 2002
>
>
>
>
> --
> Barry Isralewitz Beckman 3121 Theoretical Biophysics Group, UIUC
> Office Phone: (217) 244-1612 Home Phone: (217) 337-6364
> email: barryi_at_ks.uiuc.edu http://www.ks.uiuc.edu/~barryi 

-- 
Barry Isralewitz     Beckman 3121    Theoretical Biophysics Group, UIUC  
Office Phone: (217) 244-1612    Home Phone: (217) 337-6364
email: barryi_at_ks.uiuc.edu      http://www.ks.uiuc.edu/~barryi