RE: AW: Simulation Box Deformation

From: John Doe (helstreak_at_hotmail.com)
Date: Tue Dec 04 2012 - 06:24:09 CST

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

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.

                                               

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