Biomodeling: Analysis and Visualization

References



A case of membrane channel protein

Initial conformation in conf.pdb

traj_comp.part0001.xtc

A shell script for post-processing XTC outputs.

#!/bin/bash


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

do

    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

    fi

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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