From: Courtney Taylor (courtney.b.taylor_at_gmail.com)
Date: Fri Oct 15 2010 - 11:55:53 CDT
I did have a script to extract velocities from the binary trajectory.
I solved the problem by setting both Charmm and Namd starting velocities to
zero with the same starting coordinates, and then compared the energies.
This seemed to work.
Thanks for all the feedback.
Department of Chemical and Biomolecular Engineering
"Though the course may change sometimes the river always meets the
On Fri, Oct 15, 2010 at 7:55 AM, Werner Crous <crous.werner_at_gmail.com>wrote:
> Dear Courtney
> CHARMM does not give a velocity file in pdb format, but in binary. It is
> not clear from your post if you used a script to extract the velocities from
> a binary velocity trajectory file and wrote that in pdb format. If you did,
> then it should work. The problem is most likely that the file from CHARMM
> and the NAMD velocity file have different formats. NAMD therefore does not
> read the file at all, and therefore it starts at 0K. Rather reassign the
> Hope this helps.
> On Thu, Oct 14, 2010 at 5:09 PM, Courtney Taylor <
> courtney.b.taylor_at_gmail.com> 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 <
>> ajasja.ljubetic_at_gmail.com> wrote:
>>> 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
> Werner Crous
> Scientific Computing Research Unit
> University of Cape Town
> Rondebosch 7701
> South Africa
> Phone: +27 21 650 2530 (O)
> Fax: +27 21 686 4333
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