how to apply force SMD method on an anisotropic geometry

From: Anurag Sharma (
Date: Wed Jun 12 2013 - 15:39:34 CDT

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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