Normal Mode Analysis
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[edit] Normal procedure with GROMACS
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.
