From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Thu Feb 26 2015 - 11:42:22 CST
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 <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 LjubetiÄ*
> > <[1]ajasja.ljubetic_at_gmail.com> wrote:
> >
> > Out of curiosity -- why do you need the velocities?Â
> > 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]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]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: 773/834-2812
> > e-mail: [5]radak_at_uchicago.edu
> >
> > References
> >
> > Visible links
> > 1. mailto:ajasja.ljubetic_at_gmail.com
> > 2. mailto:brian.radak.accts_at_gmail.com
> > 3. file:///tmp/tel:773%2F834-2812
> > 4. mailto:radak_at_uchicago.edu
> > 5. 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/
>
-- 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: radak_at_uchicago.edu
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