vibrational modes calculation

From: Mortaza Aghtar (
Date: Mon Sep 23 2013 - 08:55:27 CDT

Dear all,
I have an equilibrated system that I want to calculate the vibrational
modes of it. First off all, I couldn't find any tool for it in NAMD. In
GROMACS it is possible but the Hessian matrix of atomic motions is needed.

Is it possible to calculate this matrix from namd outputs? Is there any
other tool, which is based on namd files, for principle component

Best regards,

Mortaza Aghtar
PhD Student
Jacobs University Bremen

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