From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 26 2015 - 11:03:15 CST

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]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]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/