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

From: Norman Geist (norman.geist_at_uni-greifswald.de)
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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Anurag Sharma
Gesendet: Mittwoch, 12. Juni 2013 22:40
An: namd-l_at_ks.uiuc.edu
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

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:18 CST