AW: velocity computation

From: Norman Geist (
Date: Mon Feb 08 2016 - 00:51:46 CST

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.

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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