Re: AW: Simulation Box Deformation

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 04 2012 - 11:40:26 CST

On Tue, Dec 4, 2012 at 1:24 PM, John Doe <helstreak_at_hotmail.com> wrote:
> The simulation will have PBC. I'm basically wanting to do something like:
>
> https://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Tension
> https://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression

why not use LAMMPS as shown in those wiki pages?

NAMD really wasn't made for these kind of calculations...

axel.

>
> Thanks for the input.
>
> ________________________________
> From: norman.geist_at_uni-greifswald.de
> To: helstreak_at_hotmail.com
> Subject: AW: namd-l: Simulation Box Deformation
> Date: Tue, 4 Dec 2012 07:56:43 +0100
>
> Hi John,
>
>
>
> as far as I know there’s no reflective boundaries implemented in NAMD, so if
> not using periodic boundary condition, the waters will diffuse away. But you
> can stress the box while using a barostat algorithm. Depending on what you
> want to do, you could be interested in the following:
>
>
>
> BerendsenPressure
>
> LangevinPiston
>
> outputPressure
>
> Metadynamics
>
> NamdEnergy
>
>
>
> Mit freundlichen Grüßen
>
>
>
> Norman Geist.
>
>
>
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
> von John Doe
> Gesendet: Montag, 3. Dezember 2012 22:52
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: Simulation Box Deformation
>
>
>
> Hello Users,
>
>
>
> I am wondering if it is possible to deform the simulation box in order to
> calculate uniaxel stress, either in compression or tension, and output the
> pressure on the walls of the simulation box? If so, what part of the
> documentation should I look to figure this out? This is to calculate
> mechanical response of a new water model.
>
> Thanks.

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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