Normal Mode Analysis

Normal procedure with GROMACS

In Normal Mode Analysis (NMA), calculations are run in order to study the underlying, large-scale functional motions of a macromolecule, typically a protein. The calculations require very thorough energy minimization and calculation of a Hessian matrix.

In general, both for final-stage energy minimization (with L-BFGS) and actual normal mode analysis you can use a setup with

• double-precision GROMACS installation
• switched Coulomb & van der Waals interactions; cutoffs e.g. at 1.0 nm, switched from 0.8 nm (or shifted from 0 nm).
• rlist at 1.2 to 1.3

It is imperative that you use the -t option to grompp when you create the normal mode run input file, so that you read full precision binary coordinates and not the three-decimal .gro file.

Resources

• Normal mode analysis (slides,video 1,video 2) - (Jianpeng Ma)