Re: velocity computation

From: Tristan Croll (
Date: Mon Feb 08 2016 - 12:33:16 CST

Just a thought, but you could probably hack the IMD connection to VMD quite straightforwardly to achieve this. Edit the NAMD source code to send the velocities rather than the coordinates, then in VMD:

trace add variable ::vmd_timestep(your_imd_molecule_number) write your_proc

.. and a proc to do whatever you want to do with the velocity information. As long as you're not asking VMD to actually draw anything, the back-and-forth should be fairly minimal.

From: <> on behalf of 'Patrick Welche' <>
Sent: Tuesday, 9 February 2016 12:34 AM
To: Norman Geist
Subject: Re: namd-l: velocity computation

On Mon, Feb 08, 2016 at 07:51:46AM +0100, Norman Geist wrote:
> What about NAMDs built-in velocity trajectory feature? Writing out a binary
> DCD trajectory istn't that much of a problem regarding disk space. Away from
> that, if you really want to hack the code, maybe the actual place where DCD
> trajectory files would be written might be a good place to start.

I was hoping to have shown that I have already tried all that in my first
message below:
- yes it is a problem regarding disk space
- the place where the files are written are called at the end of the time
  step, where do I get to write to some memory which doesn't disappear /
  get moved to maintain state for the next time step?



> Norman Geist
> > -----Ursprüngliche Nachricht-----
> > Von: [] Im
> > Auftrag von Patrick Welche
> > Gesendet: Freitag, 5. Februar 2016 20:05
> > An:
> > Betreff: namd-l: velocity computation
> >
> > Rather than write out a 6 TB pdb file containing velocities, just
> > to run a trivial little program over the data, I was wondering how
> > to simply keep something akin to a running sum of velocities. In a
> > non-parallel computing world, I could just grab an array, and at
> > each time step += elements in the array that would persist between
> > timesteps. What is the "correct" parallel way to do this? I see a
> > whole messaging framework. (The programmer's manual appeared to be
> > more about how the physics is implemented, and some of the classes
> > which seemed interesting from the messaging point of the view no
> > longer exist.)
> >
> > I suppose I am looking for "Hello World" where "Hello" comes from
> > the first timestep, and "World" the second...
> >
> > Cheers,
> >
> > Patrick

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