From: Wei Chen (cwbluesky_at_gmail.com)
Date: Mon Mar 22 2010 - 16:25:50 CDT
Hi,
You messed up the temperature command with the temperature variable.
You do need the temperature variable as "set temperature <your
temperature>".
But you should comment out the temperature command as "temperature <your
temperature>" when you read in a velocity restart file. The temperature
command only sets the starting temperature.
Wei Chen
On Mon, Mar 22, 2010 at 1:50 PM, neville forlemu
<neville_forlemu_at_yahoo.com>wrote:
> Hello
>
> I am new to NAMD and have a question about restarting jobs with the
> velocity restart file.
>
>
>
> The manuals and tutorials mention that when restarting a job with the
> velocit file you need to turn off the temperature variable.
>
>
>
> However if you need to do and NPT simulation, say with a langevin coupling
> then you do need the temperature variable.
>
>
>
> So my question therefore is to know whether the velocity restart file
> keeps this information so that you can turn off the Langevin Temp
> Control and Pressure control variable?
>
>
>
> I will appreciate some help on this
>
> Thanks
>
> Neville
>
>
> --- On Wed, 2/24/10, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Subject: Re: namd-l: psfgen error
> To: "Syed Kashif Zafar" <skashifzafar_at_yahoo.com>
> Cc: namd-l_at_ks.uiuc.edu
> Date: Wednesday, February 24, 2010, 12:19 AM
>
> On Tue, Feb 23, 2010 at 11:44 PM, Syed Kashif Zafar
> <skashifzafar_at_yahoo.com> wrote:
> > Hi all,
> > I have an equilibrated pdb patch for a DMPC bilayer. Now I want to add
> > water and run it using NAMD.But in the pdb patch the molecules are
> wrapped
> > and when I use psfgen and topology file to generate the psf, it connects
> > the atoms across the periodic cell giving bonds that exist across the
> > periodic cell. Can anyone suggest how I can unwrap the coordinates in the
> > pdb that I have or some other solution.
>
> actually, there is no real problem if you use the same simulation cell size
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