1.1 Descriptors of dynamics

Generating vectors describing protein dynamics from the MD ensemble

Using your favourite programming tool (GROMACS/VMD/AMBERTools/MDAnalysis/mdtraj) extract vector(s) (v_i....v_n), stored in an ascii file format (xvg or txt or dat), which describe/capture the dynamics of the system. The format of the file is described below.

The popular choices for such vector(s) are distance between two atoms or a group of atoms, projections on the principal components.

The first column should be time stamp (t) or frame number and from the second column, each column will be one of the dynamics vector (d1...dn), with no header

The following file has one time (t) column and three dynamics vectors (v₁,v₂,v₃).

0 1.2 4.3 13045.92
20 1.12 4.13 13135.12
40 0.2 1.2 12126.21