AW: Loading Velocity DCD file

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Dec 18 2014 - 02:31:16 CST

Hi,

VELDCD are of the same format as the normal coordinate DCD, so you can simply load them as any other DCD file. The only difference is that instead of coordinates you will find the velocities in the x y z information, and a VELDCD doesn't contain box information (charmm extra block). For your analysis you could of course load them both to the same molecule, but I guess using two molecules, one for coordinates and one for velocities might be the better choice.

Norman Geist.

> -----Urspr√ľngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von JAVAD NOROOZI
> Gesendet: Mittwoch, 17. Dezember 2014 20:23
> An: NAMD list
> Betreff: namd-l: Loading Velocity DCD file
>
> Dear users,
> I have a couple of questions regarding loading a #### .veldcd file?
>
> 1.The tutorial has a an example of loading ###.vel file which is for a
> single frame, wondering how to load a velocity trajectory , like the
> one for the coordinate dcd file(i tried to browse ###.veldcd inot VMD ,
> but i get file type error)?2. I want to calculate a quantity requiring
> both the velocity and coordinate trajectories , is it possible to load
> both ###.dcd and ###.veldcd of atom selections into VMD?3.I just can
> not figure out a for loop running on both the ###.dcd and ###.veldcd
> files loaded into VMD=

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