Gaucher Task10 Protocol

Sources

You can checkout the git repository containing all relevant data an scripts by:

git clone /mnt/home/student/angermue/mp/tasks/task10

Checking the results

gmxcheck -f traj.xtc 

Visualizing the results

Given the reference structure $REF, we corrected the trajectory file $TRAJ.xtc as follows:

echo 0 | trjconv -f $TRAJ.xtc -s $REF -pbc nojump -o ${TRAJ}_nojump.xtc
echo 1 0 | trjconv -f ${TRAJ}_nojump.xtc -s $REF -center -o ${TRAJ}_center.xtc
echo 1 0 | trjconv -f ${TRAJ}_center.xtc -s $REF -fit rot+trans -o ${TRAJ}_norot.xtc

Next, we created a PDB file with several states using the time resolution $TIME=10:

echo 1 |trjconv -f ${TRAJ}_norot.xtc -s $REF -o ${TRAJ}_traj.pdb
echo 1 | g_filter -f ${TRAJ}_traj.pdb -s $REF -ol ${TRAJ}_traj_$TIME.pdb -fit -nf $TIME

Quality assurance

Thermodynamic parameters

echo "12 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_temp.xvg > $A/${NAME}_temp.out
echo "13 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_pres.xvg > $A/${NAME}_pres.out
echo "11 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_tot.xvg > $A/${NAME}_tot.out
echo "9 0" | g_energy -f $M/${NAME}_md.edr -o $A/${NAME}_pot.xvg > $A/${NAME}_pot.out

Root Mean Square Deviation

echo 1 1 | g_rms -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_p_start.xvg
echo 4 4 | g_rms -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_b_start.xvg
echo 1 1 | g_rms -f ${MB}_norot.xtc -s ${A}/${NAME}_rmsf_p_avg.pdb -o ${AB}_p_avg.xvg
echo 4 | g_rmsdist -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_b.xvg

Radius of gyration

echo 1 | g_gyrate -f ${MB}_norot.xtc -s $MB.tpr -o $AB.xvg

Minimum distance between periodic boundary cells

echo 1 | g_mindist -f $M/${NAME}_md_norot.xtc -s $M/${NAME}_md.tpr -od $A/${NAME}_mindist_p.xvg -pi > $A/${NAME}_mindist_p.out
echo 3 | g_mindist -f $M/${NAME}_md_norot.xtc -s $M/${NAME}_md.tpr -od $A/${NAME}_mindist_c.xvg -pi > $A/${NAME}_mindist_c.out

RMSF

echo 3 | g_rmsf -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_c.xvg -ox ${AB}_c_avg.pdb -oq ${AB}_c_bfac.pdb -res > ${AB}_c.out
echo 1 | g_rmsf -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_p.xvg -ox ${AB}_p_avg.pdb -oq ${AB}_p_bfac.pdb -res > ${AB}_p.out

Hydrogen bond network

echo 1 1 | g_hbond -f ${MB}_norot.xtc -s $MB.tpr -num ${AB}_pp.xvg
echo 1 12 | g_hbond -f ${MB}_norot.xtc -s $MB.tpr -num ${AB}_pw.xvg

Solvent Accessibility Surface

echo 1 1 | g_sas -f ${MB}_norot.xtc -s $MB.tpr -o ${AB}_all.xvg -or ${AB}_res.xvg -oa ${AB}_at.xvg

Ramachandran plot

g_rama -f ${MB}_norot.xtc -s $MB.tpr -o $AB.xvg

Analysis of dynamics and time-averaged properties

echo 6 6 | g_cluster -s $MB.tpr -f ${MB}_norot.xtc -dm $A/${NAME}_rms.xpm -dist ${AB}_distrib.xvg \
                     -o ${AB}_clusters.xpm -sz ${AB}_sizes.xvg -tr ${AB}_transbox.xpm -ntr ${AB}_trans.xvg \
                     -clid ${AB}_time.xvg -cl ${AB}_clusters.pdb -cutoff $C -method gromos -dt 10 -minstruct 50