From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 26 2015 - 12:47:52 CST

Hi,
  The psfgen utility began as a standalone program, but very early on
it was modified to add Tcl command bindings, allowing it to be
dynamically loaded into VMD as a Tcl package. The standalone and
VMD Tcl-versions of psfgen are both compiled from exactly the same
source code. The psfgen code is maintained by Jim Phillips, the lead
NAMD developer. As you mention psfgen is by far most commonly used
within VMD, but that being said, there's nothing preventing it from
loaded into other Tcl interpreters, and it should even be possible to
run the same Tcl-based version from VMD within NAMD if one wanted to.

Cheers,
  John

On Thu, Feb 26, 2015 at 11:42:22AM -0600, Brian Radak wrote:
> Sorry, in retrospect I realize that was a rude/aggravating response.
>
> It hasn't been clear to me who maintains psfgen, which is why I posted to
> both lists. Are VMD's PSF building capabilities separate from psfgen or is
> the code base the same? It would seem that most people use autopsf to
> build their systems for NAMD, but the NAMD manual seems to give primacy to
> the command line psfgen utility that ships with it (although even that
> example involves using VMD to extend its capabilities).
>
> Brian
> On Thu, Feb 26, 2015 at 11:03 AM, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Brian,
> ┬ Ah, I assumed that you were intent on using VMD since you posted your
> question to the VMD-L mailing list.┬ In the future, I'd suggest not
> cross-posting if your questions are not VMD related, it will save
> all of us a lot of time and energy.
>
> Cheers,
> ┬ John
> On Thu, Feb 26, 2015 at 10:56:57AM -0600, Brian Radak wrote:
> >┬ ┬ I would like to retain the velocities of all of the existing
> atoms. Only
> >┬ ┬ the new atoms need to get new velocities.
> >
> >┬ ┬ As to John's solution, unfortunately I'd like to keep VMD out of
> this, as
> >┬ ┬ my goal is to do all of this in a single namd configuration file
> using
> >┬ ┬ psfgen. This whole process will need to be done repeatedly and
> on-the-fly
> >┬ ┬ during a simulation.
> >
> >┬ ┬ Brian
> >┬ ┬ On Thu, Feb 26, 2015 at 10:37 AM, Ajasja Ljubeti├**
> >┬ ┬ <[1][2]ajasja.ljubetic_at_gmail.com> wrote:
> >
> >┬ ┬ ┬ 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,
> >┬ ┬ ┬ Ajasja
> >┬ ┬ ┬ On 26 February 2015 at 16:41, Brian Radak
> >┬ ┬ ┬ <[2][3]brian.radak.accts_at_gmail.com> 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: [3]773/834-2812
> >┬ ┬ ┬ ┬ e-mail: [4][4]radak_at_uchicago.edu
> >
> >┬ ┬ --
> >┬ ┬ 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: [5]773/834-2812
> >┬ ┬ e-mail: [5][6]radak_at_uchicago.edu
> >
> > References
> >
> >┬ ┬ Visible links
> >┬ ┬ 1. mailto:[7]ajasja.ljubetic_at_gmail.com
> >┬ ┬ 2. mailto:[8]brian.radak.accts_at_gmail.com
> >┬ ┬ 3. file:///tmp/tel:773%2F834-2812
> >┬ ┬ 4. mailto:[9]radak_at_uchicago.edu
> >┬ ┬ 5. mailto:[10]radak_at_uchicago.edu
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [11]http://www.ks.uiuc.edu/~johns/┬ ┬ ┬ ┬ ┬ ┬ Phone:
> [12]217-244-3349
> [13]http://www.ks.uiuc.edu/Research/vmd/
>
> --
> 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: [14]radak_at_uchicago.edu
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:ajasja.ljubetic_at_gmail.com
> 3. mailto:brian.radak.accts_at_gmail.com
> 4. mailto:radak_at_uchicago.edu
> 5. file:///tmp/tel:773%2F834-2812
> 6. mailto:radak_at_uchicago.edu
> 7. mailto:ajasja.ljubetic_at_gmail.com
> 8. mailto:brian.radak.accts_at_gmail.com
> 9. mailto:radak_at_uchicago.edu
> 10. mailto:radak_at_uchicago.edu
> 11. http://www.ks.uiuc.edu/~johns/
> 12. file:///tmp/tel:217-244-3349
> 13. http://www.ks.uiuc.edu/Research/vmd/
> 14. mailto:radak_at_uchicago.edu

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/