# Calculates Normal Modes using Go-like Energy Model and Delaunay-defined neighbours for very large PDB files (beta version)

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This form will submit a Normal Modes calculation on the given input PDB file.

**Input:**

You need at least one pdb file to calculate Normal Modes using variants of the Elastic Network Model.
No cutoff is needed if you use the Delaunay tessalation to define neighbours.

You can also define the regular ENM with a cutoff, and do NMA in a new version based on Krylov space,
written by Patrice Koehl, that accepts structures with a very large number of atoms (e.g. 100,000).

**Output:**

There will be one output PDB file per mode, named **traj_mode#.pdb**, directly loadable by
PyMol or
VMD.

**References:**

Article_1

Article_2

Here we use an expanded Energy Model, the so-called Go-model, to calculate the Normal Modes. It contains an elastic term on the bond lengths, two elastic terms based on 3-atoms (torsional) and 4-atoms (dihedral) angles, and a non-local-term (vdw-like).

${V}_{\mathrm{tot}}={V}_{\mathrm{bond}}+{V}_{\mathrm{tor}}+{V}_{\mathrm{dihed}}+{V}_{\mathrm{non-local}}$

The neighbours are defined either by Delaunay triangulation (no cutoff) or with a cutoff criterion.