Re: vmd-l: velocity IO with psfgen?

From: John Stone (
Date: Thu Feb 26 2015 - 10:24:36 CST

  I believe you should be able to do what you're describing without the help
of psfgen, just by using atom selections in VMD. You can have VMD
load the existing coordinates and velocities, and then prune,
rearrange, or create new ones which are associated with your newly-built
PSF from psfgen, and then write out all of these to new files.

  John Stone

On Thu, Feb 26, 2015 at 09:41:04AM -0600, Brian Radak wrote:
> 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: [1]
> References
> Visible links
> 1.

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