Re: Namd using Charmm restart files

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:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4125.html

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
(225)-771-8554
(615)-343-3257

"Though the course may change sometimes the river always meets the
sea"--Zeppelin

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.
>
> Regards,
> Ajasja
>
> On Wed, Oct 13, 2010 at 23:55, Courtney Taylor <
> courtney.b.taylor_at_gmail.com> wrote:
>
>> All,
>>
>> 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??
>>
>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0191.html
>>
>> Courtney Taylor
>> PhD Candidate
>> Department of Chemical and Biomolecular Engineering
>> Vanderbilt University
>> (225)-771-8554
>> (615)-343-3257
>>
>> "Though the course may change sometimes the river always meets the
>> sea"--Zeppelin
>>
>>
>

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