AW: Simulation Box Deformation

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Dec 04 2012 - 00:57:13 CST

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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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