From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Oct 14 2010 - 14:28:09 CDT
Try running for 0 steps with binary output turned off. Does the .vel pdb
file that is output match the one you used as input? Then try starting
with "temperature 300" instead of velocities. Are the output velocities
on the same scale as your CHARMM file? If they are off by a factor of 20
or 400 then you're doing the unit conversion backwards.
On Thu, 14 Oct 2010, Courtney Taylor wrote:
> 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?
> Courtney Taylor
> PhD Candidate
> Department of Chemical and Biomolecular Engineering
> Vanderbilt University
> "Though the course may change sometimes the river always meets the
> On Thu, Oct 14, 2010 at 1:31 AM, Ajasja Ljubetič
>> 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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:12 CST