Re: velocity IO with psfgen?

From: Ajasja Ljubetič (
Date: Thu Feb 26 2015 - 10:37:55 CST

Out of curiosity -- why do you need the velocities?
NAMD can always assign new (random) velocities from the Maxwell-Boltzmann
distribution using the temperature command.

Best regards,

On 26 February 2015 at 16:41, Brian Radak <>

> Would it be difficult/possible to implement reading/writing of velocity
> files with psfgen? I'm assuming that the underlying binary format for .coor
> and .vel files is the same and thus the reading/writing is only really
> different in the presumed meaning of the arrays. Is this correct?
> What I'd like to be able to do is read in a psf/coor/vel combination, add
> new atoms with a patch and then write a new psf/coor/vel combination to
> disk.
> Psfgen can already assign new coordinates to new atoms and I again assume
> it would be much the same mechanism to assign velocities (an analog of the
> "coord" command). It would also be convenient to simply draw new velocities
> from a Maxwell-Boltzmann distribution at a given temperature.
> I'm poking around in "tcl_psfgen" at the moment, but not entirely sure
> what to make of everything.
> Thanks,
> Brian
> --
> Brian Radak
> Postdoctoral Scholar
> University of Chicago
> Department of Biochemistry & Molecular Biology
> Gordon Center for Integrative Science, W323A
> 929 E. 57th St.
> Chicago, IL 60637-1454
> Tel: 773/834-2812
> e-mail:

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