Normal Mode simulation of biomolecules

Normal Modes and Molecular Dynamics

Information

Simulation

Normal Mode Langevin

User Simulation Submission

About us

NAME="jmv1"

Normal Mode Simulator.
This simulator is designed to allow the user to visualize motions along the normal modes generated from a mass-weighted Hessian. In the 'Analytic' mode the simulator sequentially moves the molecule along a user defined set of modes solved analytically. In the 'Molecular Dynamics' mode only dynamics in the user defined space of the selected modes is propagated.

Visual controls.
The viewer can be controlled using the mouse. By left-clicking and dragging the mouse the molecule can be rotated.

Simulation. To run a new simulation select the required parameters.

Information on Normal Mode Langevin.

This website illustrates the Normal-Mode-Partitioned Langevin dynamics integrator called NML.

The aim of NML is to approximate the kinetics or thermodynamics of a biomolecule by a reduced model based on a normal mode decomposition of the dynamical space. Our basis set uses the eigenvectors of a mass re-weighted Hessian matrix calculated with a biomolecular force field. Low frequency eigenvalues correspond to more collective motions, whereas the highest frequency eigenvalues are the limiting factor for the stability of the integrator. The higher frequency modes are overdamped and relaxed near to their energy minimum while respecting the subspace of low frequency dynamical modes. Numerical results confirm that both sampling and rates are conserved for an implicitly solvated alanine dipeptide model, with only 30% of the modes propagated, when compared to the full model. For implicitly solvated systems the method can be shown to give improvements in efficiency more than 2 times even for sampling a small 22 atom (alanine dipeptide) model and in excess of an order of magnitude for sampling an 882 atom (bovine pancreatic trypsin inhibitor, or BPTI) model, with good scaling with system size subject to the number of modes propagated. This is illustrated in the graph below showing 'speedup' (the ratio of the highest frequency in the system to the highest frequency in the set of modes):

This website allows the user to explore the NML integrator using two molecular models; alanine dipeptide and BPTI. By selecting the modes of interest it is possible to see the effects of the coarse graining, either using the analytical solution of the discreet quadratic solution or molecular dynamics in the subspace spanned by the modes.

NML has been implemented in the open source software ProtoMol.

Christopher R. Sweet

Assistant Research Professor
Department of Computer Science and Engineering
University of Notre Dame
IN 46556.

Paula M. Petrone

Graduate student
Biophysics Dept.
Stanford University
CA 94305.

Vijay S. Pande

Associate Professor of Chemistry and of Structural Biology
Stanford University
CA 94305.

Jesús A. Izaguirre

Associate Professor
Department of Computer Science and Engineering
University of Notre Dame
IN 46556.

Web design by
Christopher R. Sweet & James C. Sweet

Java Applet design by
Christopher R. Sweet & James C. Sweet
Applet built using Java bindings for OpenGL (JOGL)

Submit About the User Submission system.

The submission system is provided for users to generate the appropriate eigenvector and configuration files to run simulations using the Open-Source Protomol molecular dynamics (MD) package. The system requires both a Protein Data Bank (PDB) file and a structure (PSF) file. The PDB file must be complete, and include all Hydrogen atoms. Tools, such as VMD, are available for adding Hydrogen atoms to the PDB file and the generation of PSF files. After submitting the files the system will provide the user with a table of step sizes that are appropriate for a given number of modes. The user selects the required number of modes/stepsize (the level of time coarse graining) and the Protomol configuration file and eigenvector file will be generated.

Click here to use the User Submission system