Task 10 - Journal (PKU)

Initial checks

Verify completion, frame number and frame rate: <source lang="bash"> gmxcheck -f _md.xtc </source>

performance statistics: <source lang="bash"> tail _md.log </source>

Create Trajectories

<source lang="bash">

1. fix jumps over the periodic boundary

trjconv -f _md.xtc -s _solv.pdb -pbc nojump -o _traj_nojump.xtc<<EOF0\nEOF

1. center protein in the box

trjconv -f _traj_nojump.xtc -s _solv.pdb -center -o _traj_center.xtc<<EOF1\n0\nEOF

1. eliminate rotations

trjconv -f _traj_center.xtc -s _solv.pdb -fit rot+trans -o _traj_norot.xtc<<EOF1\n0\nEOF

1. create pdb file

trjconv -f _traj_norot.xtc -s _solv.pdb -o _traj.pdb<<EOF1\nEOF

1. reduce fluctuations and write every fifth frame

g_filter -f _traj.pdb -s _solv.pdb -ol _traj_filtered.pdb -fit -nf 5<<EOF1\nEOF

</source>

Plot Energies

<source lang="bash"> echo 12 0 | g_energy -f _md.edr -o _temperature.xvg echo 13 0 | g_energy -f _md.edr -o _pressure.xvg echo -e "9\n10\n11 0" | g_energy -f _md.edr -o _energy.xvg echo 18 0 | g_energy -f _md.edr -o _volume.xvg echo 19 0 | g_energy -f _md.edr -o _density.xvg echo -e "15\n16\n17 0" | g_energy -f _md.edr -o _box.xvg echo -e "48\n50 0" | g_energy -f _md.edr -o _coulomb-inter.xvg echo -e "49\n51 0" | g_energy -f _md.edr -o _vanderwaals-inter.xvg </source>

Minimal Distance of Interactions

<source lang="bash"> echo 1 0 |g_mindist -f _md.xtc -s _md.tpr -od _minimal_periodic_distance.xvg -pi echo 3 0 |g_mindist -f _md.xtc -s _md.tpr -od _minimal_periodic_c_alpha_distance.xvg -pi </source>

RMSD Calculations

<source lang="bash"> echo -e "1\n1 0"|g_rmsf -f _md.xtc -s _md.tpr -o _rmsf-per-residue.xvg -ox _average.pdb -oq _bfactors.pdb -res echo 1 0 |g_rms -f _traj_norot.xtc -s _md.tpr -o _rmsd-all-atom-vs-start.xvg echo 4 0 |g_rms -f _traj_norot.xtc -s _md.tpr -o _rmsd-backbone-vs-start.xvg echo 1 |trjconv -f _traj_norot.xtc -s _md.tpr -o _protein.xtc echo -e "1\n1 0" |g_rms -f _protein.xtc -s _average.pdb -o _rmsd-all-atom-vs-average.xvg echo -e "4\n4 0" |g_rms -f _protein.xtc -s _average.pdb -o _rmsd-backbone-vs-average.xvg </source>

Radius of Gyration

<source lang="bash"> echo 1 0 |g_gyrate -f _traj_norot.xtc -s _md.tpr -o _radius-of-gyration.xvg echo 1 0 |g_gyrate -f _traj_norot.xtc -s _md.tpr -o _moments_of_inertia.xvg -moi </source>

Accessible Surface

<source lang="bash"> echo 1 1 |g_sas -f _traj_norot.xtc -s _md.tpr -o _solvent-accessible-surface.xvg -oa _atomic-sas.xvg -or _residue-sas.xvg </source>

Hydrogen Bonds

<source lang="bash"> echo 1 1 | g_hbond -f _traj_norot.xtc -s _md.tpr -num _hydrogen-bonds-intra-protein.xvg echo 1 12 | g_hbond -f _traj_norot.xtc -s _md.tpr -num _hydrogen-bonds-protein-water.xvg </source>

Saltbridges

<source lang="bash"> g_saltbr -f _traj_norot.xtc -s _md.tpr -t 0.5 -sep </source>

Secondary Structure

Gromacs can't handle current dssp versions (compare). If anyone finds a solution to this, do tell.

Ramachandran Plot

<source lang="bash"> g_rama -f _traj_norot.xtc -s _md.tpr -o _ramachandran.xvg </source>

more RMSDs

<source lang="bash"> echo -e "1\n1\n\n"|g_rms -s _md.tpr -f _traj_norot.xtc -f2 _traj_norot.xtc -m _rmsd-matrix.xpm -dt 10 echo -e "6\n6\n\n"|g_rms -s _md.tpr -f _traj_norot.xtc -f2 _traj_norot.xtc -m _rmsd-matrix_chain-c_b.xpm -dt 10 xpm2ps -f _rmsd-matrix.xpm -o _rmsd-matrix.eps -rainbow blue xpm2ps -f _rmsd-matrix_chain-c_b.xpm -o _rmsd-matrix_chain-c_b.eps -rainbow blue </source>

Cluster Analysis

<source lang="bash"> echo 6 6 | g_cluster -s _md.tpr -f _traj_norot.xtc -dm _rmsd-matrix_chain_c_b.xpm -dist _rmsd-distribution.xvg -o _clusters.xpm -sz _cluster-sizes.xvg -tr _cluster-transitions.xpm -ntr _cluster-transitions.xvg -clid _cluster-id-over-time.xvg -cl _clusters.pdb -cutoff 0.1 -method gromos -dt 10 </source>

Distance RMSD

<source lang="bash"> echo 1|g_rmsdist -s _md.tpr -f _traj_norot.xtc -o _distance-rmsd.xvg </source>