VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Tue May 24 2016 - 10:57:58 CDT

Thank you so much!

2016-05-24 17:55 GMT+02:00 Maxim Belkin <mbelkin_at_ks.uiuc.edu>:

> Hi Laura,
>
> > On May 24, 2016, at 10:41, Laura Joana <laurajoanalopes_at_gmail.com>
> 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
>
>
> Maxim