From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Thu Feb 26 2015 - 10:56:57 CST
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.
On Thu, Feb 26, 2015 at 10:37 AM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com
> 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,
> On 26 February 2015 at 16:41, Brian Radak <brian.radak.accts_at_gmail.com>
>> 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
>> e-mail: 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: radak_at_uchicago.edu
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