Re: Restarting A NAMD job with velocity file

From: neville forlemu (neville_forlemu_at_yahoo.com)
Date: Thu Mar 25 2010 - 21:59:01 CDT

Hello,
I understand NAMD2.7b2 has the metadynamics patch
included. I was wondering whether somebody who has used it before can
comment on how well it speeds up convergence of rare events, and
secondly whether one can use a multiple walker strategy with this
metadynamics colvar module as is implemented in the NAMD/PLUMED
compilation.

Thanks
Neville

________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_temple.edu>
To: neville forlemu <neville_forlemu_at_yahoo.com>
Cc: Axel Kohlmeyer <akohlmey_at_gmail.com>; namd-l_at_ks.uiuc.edu
Sent: Mon, March 22, 2010 6:30:00 PM
Subject: Re: namd-l: Restarting A NAMD job with velocity file

Hello Neville, "temperature" means the initial temperature, and
"langevinTemp" (if you use Langevin) is the temperature that you want
the thermostat to keep. The instantaneous temperature will be around
it.

If you provide with velocities, the instantaneous temperature will be
calculated from the velocities, and that's why "temperature" should
not be used, to not override that information.

Giacomo

---- ----
Giacomo Fiorin
   ICMS - Institute for Computational Molecular Science
     Temple University
     1900 N 12 th Street, Philadelphia, PA 19122
work phone: (+1)-215-204-4216
mobile: (+1)-267-324-7676
mail: giacomo.fiorin_at_gmail.com
---- ----

On Mon, Mar 22, 2010 at 4:50 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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