Biomodeling: Analysis and Visualization

Intro

In trjconv/conf.pdb, you can find a system with a tetrameric membrane channel embedded in a lipid bilayer.
gmx mdrun will generate trajectory files, such as traj_comp.part0001.xtc.
- An example is uploaded as traj_comp.part0001.xtc
Loading traj_comp.part0001.xtc to VMD will show a messy conformation.
Post-processing the XTC files is useful for analysis and visualization.

Initial conformation in conf.pdb

traj_comp.part0001.xtc

#!/bin/bash

for i in traj_comp.part????.xtc # initial XTC files with 20 ps time step.

o=$(echo $i | sed "s/.xtc/.1ns.xtc/")

if [ $i -nt $o ]

then

echo "Protein 0" | gmx trjconv -s topol.tpr -f $i -o $o -pbc mol -ur compact -center -skip 50

done

rm -f all*xtc

echo 0 | gmx trjcat -f traj_comp.part????.1ns.xtc -o all.1ns.xtc #-cat

rm -f *tmp* *#*

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