AW: how to apply force SMD method on an anisotropic geometry

From: Norman Geist (
Date: Thu Jun 13 2013 - 01:56:48 CDT

Hi Anurag,


if you mean pressure as force on the boundaries, this could be done using
one of the barostat (langevinpiston or berendsen I guess) algorithms.


Also, have you thought about using dummy atoms to get such a plane that you
talked about, or what exactly is the problem, what's the molecules shape and
where to you want to apply the force?


Norman Geist.


Von: [] Im Auftrag
von Anurag Sharma
Gesendet: Mittwoch, 12. Juni 2013 22:40
Betreff: namd-l: how to apply force SMD method on an anisotropic geometry


Dear all users,

        I am working on a solvated model (protein surrounded by water
molecules) which has anisotropic geometry. I am trying to apply force
constant method (SMD) to calculate stresses and modulus of the system. In
force constant method one applies force on individual atoms placed in a
layer but due to anisotropic geometry I don't know how can I achieve this.

Another possible way to calculate stresses is to put solvated system in a
box and then apply force on the boundaries of that box. Is there any method
in NAMD which I can use here.


Thank in advance.


Anurag Sharma

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