From: Maxim Belkin (
Date: Tue May 24 2016 - 10:55:28 CDT

Hi Laura,

> On May 24, 2016, at 10:41, Laura Joana <> wrote:
> Dear all,
> Before my question: I'm looking for a command line solution as I'm writing a script for VMD!
> Is there a way to write a velocity binary file (.vel) from a dcd file using VMD?

No. Trajectory file contains information about position of atoms. DCD files know nothing about velocities.
In NAMD you can enable output of velocity-trajectory files by setting vecdcdfreq variable (which is similar to dcdfreq).
In that case, NAMD will output .veldcd files that you can then use to output binary velocity files.

> There are no commands in the VMD user guide to write coordinates and velocities binary files. After some research I found the command "writenamdbin", used to write a coordinate binary file after using the atomselect command (I can choose the frame with that, so it seams nice). But, as I can not find any documentation about that command I don't really know how to use it. Does this command writes velocity binary files also?

1. Load a PSF file
2. Load a (velocity-)trajectory file
3. Make a selection like so: set sel [atomselect top "all"]
4. Output binary velocity file like so: $sel writenamdbin outputfile.vel
5. Enjoy.

> Bests,
> Laura