From: Courtney Taylor (courtney.b.taylor_at_gmail.com)
Date: Thu Oct 14 2010 - 10:09:34 CDT
Thanks for the reply. I understand what units are being used. I also
understand that NAMD velocity, except when written to pdb format, needs to
be multiplied by a timefactor, as described in this post:
The issue I have is when I take a pdb velocity file from CHARMM and try to
use it as the NAMD velocity input, NAMD begins with a temperature of 0
Kelvin when it should begin closer to 300 K. Any thoughts on this?
Department of Chemical and Biomolecular Engineering
"Though the course may change sometimes the river always meets the
On Thu, Oct 14, 2010 at 1:31 AM, Ajasja LjubetiÄ
> As allways, everything is in the UG<http://www.ks.uiuc.edu/Research/namd/2.7b4/ug/node13.html>
> The standard units used by NAMD are Angstroms for length, kcal/mol for
> energy, Kelvin for temperature, and bar for pressure. Wallclock or CPU times
> are given in seconds unless otherwise noted.
> But personally I don't see any problem with reassigning velocities.
> On Wed, Oct 13, 2010 at 23:55, Courtney Taylor <
> courtney.b.taylor_at_gmail.com> wrote:
>> I have looked through the forums and found no response to this issue of
>> Namd starting at 0 Kelvin when using a Charmm velocity pdb as a starting
>> point. Has anyone seen this again, or does anyone know how to resolve this??
>> Courtney Taylor
>> PhD Candidate
>> Department of Chemical and Biomolecular Engineering
>> Vanderbilt University
>> "Though the course may change sometimes the river always meets the
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