Tools: Python and Tcl.

Purpose: to calculate the minimum distance between membrane lipid molecules for all frames of trajectory.

Molecular system: lipid bilayer system with transmembrane molecules.

step1:

dcd_unwrap.tcl: to unwrap molecular dynamics simulation trajectories.

vmd -dispdev none

vmd> source dcd_unwrap.tcl

catdcd -o dppc_p.xyz -otype xyz -stype pdb -s ../dppc_p.pdb dppc_p.dcd

step2:

dist_nearest_neighbor.py: to plot time series and histograms of all pairs of DPPC P atoms that are initially nearest neighbors.

./dist_nearest_neighbor.py dppc_p.xyz 1 -1

or

./dist_nearest_neighbor.py dppc_p.xyz framenum1 framenum2

for user-defined framenum1 and framenum2

./dist_nearest_neighbor.py test.xyz 1 -1