VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 02 2015 - 15:22:07 CST

Hi,
  I brought up this issue with Jim, and it seems like we could make a small
change to the namdbin plugin so that it assumes that a file contains velocities
if the file extension is set to .vel, which would eliminate the need to do
various post-processing to get the desired result when reading in velocities.

Let me know what you guys think about this. I'm not aware of any downside...

Cheers,
  John

On Wed, Dec 02, 2015 at 01:14:37PM -0600, Josh Vermaas wrote:
> Hi Ben,
>
> From my understanding, .vel files have the same format as the .coor files
> NAMD emits. So to simply load the files into VMD isn't a big deal, "mol
> addfile type namdbin blah.vel" will load the velocities of all the atoms
> as though they were coordinates. This makes the structure look like a
> pincushion, and usually isn't very informative. What I've done in the
> past, just to get a sense of what atoms are moving quickly, is to
> calculate the speed of each atom, put it into the user field, and see what
> it looks like in the structure.
>
> #Load the coordinates to localize the atoms
> mol new coordinates.pdb
> #Load the velocities. Your molecule will now have 2 frames, one that is
> coordinates, one that is velocities.
> mol addfile type namdbin blah.vel
> #Set beta or user or whatever to the square of the speed.
> set speedsel [atomselect top "all" frame 1]
> set speedsquared [vecadd [vecmul [$speedsel get x] [$speedsel get x]]
> [vecmul [$speedsel get y] [$speedsel get y]] [vecmul [$speedsel get z]
> [$speedsel get z]]]
> $speedsel set beta $speedquared
>
> -Josh Vermaas
>
> On 12/02/2015 11:42 AM, Ben Rousseau wrote:
>
> Greetings,
>
> I read this was a work in progress a few years ago, but I haven't found
> any information\001since then: Is there a way to load a NAMD output .vel
> file into vmd?\001
>
> Thank you,
>
> Ben 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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