CD task10 protocol

Script with all analysis steps

1. 1. !/bin/bash

1. wildtype

path=/opt/SS12-Practical/gromacs/bin/ EDR="2O4H_chainA_md" MUT="wt"

1. gmxcheck

$path gmxcheck -c $EDR.tpr gmxcheck -f $EDR.xtc

1. pymol visualization

echo 1 0| trjconv -s $EDR.tpr -f $EDR.xtc -o $MUT_vis.pdb -pbc nojump -dt 10

1. energy

echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy

1. a305e

EDR="A305E_scwrl_mini_md" MUT="A305E_scwrl"

echo 12 0| g_energy -f $EDR.edr -o $MUT.temp.xvg echo 13 0 | g_energy -f $EDR.edr -o $MUT.pressure.xvg echo 9 0| g_energy -f $EDR.edr -o $MUT.potential.xvg echo 11 0 | g_energy -f $EDR.edr -o $MUT.totenergy.xvg