From: Brian Radak (
Date: Thu Feb 26 2015 - 09:41:04 CST

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

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.


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