CD task10 protocol

Script with all analysis steps

##!/bin/bash

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

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

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

#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 
  

#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