Molecular Dynamics Analysis BCKDHA

A brief check of results

To verified that the simulations finished properly we first use the command

• gmxcheck -f wt.xtc

How many frames are in the trajectory file and what is the time resolution?

• frames: 2001
• time resolution: 5ps

How long did the simulation run in real time (hours), what was the simulation speed (ns/day) and how many years would the simulation take to reach a second?

• real time: 9h27:35
• simulation speed: 25.370 ns/day
• simulation speed: 107991 years/second

Which contribution to the potential energy accounts for most of the calculations?

• potential energy: -1.24431e+06

Visualization of results

To get a pdb file to be able to visualize the model with pymol we used the Swiss army knife gromacs tool trjconv:

• trjconv -s wt.tpr -f wt.xtc -o protein.pdb -pbc nojump -dt 10

Quality assurance

Energy calculations

To calculate the different energies we used the command:
g_energy -f wtMD.edr -o energy.xvg
After submitting this command we had to choose the energy which should calculated.

• Pressure: 13
• Temperature: 12
• Potential: 9
• Total Energy: 11

Pressure

Energy Average Err.Est. RMSD Tot-Drift (bar) Pressure 1.01601 0.015 71.2152 -0.0706383

Temperature

Energy Average Err.Est. RMSD Tot-Drift (K) Temperature 297.941 0.0047 0.954498 0.00557078

Potential

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol) Potential -1.24431e+06 66 1041.57 -463.992

Total Energy

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol) Total Energy -1.02119e+06 65 1279.76 -459.819

Minimum distance between periodic boundary cells

To calculate the minimum distance we used the command
g_mindist -f wtMD.xtc -s wtMD.tpr -od minimal-periodic-distance.xvg -pi
After submitting this command we chose group 1 to calculate the minimum distance for the whole protein.

Shortest periodic distance is 1.40945 (nm) at time 6090 (ps) between atoms 25 and 6490.

Root mean square fluctuations

To calculate the minimum distance we used the command
g_rmsf -f wtMD.xtc -s wtMD.tpr -o rmsf-per-residue.xvg -ox average.pdb -oq bfactors.pdb -res
After submitting this command we had to choose the group we want the RMSF to be calculated for:

• Protein: 1
• C-alpha: 3

RMSF for protein

RMSF for C-alpha

Pymol analysis of average and bfactor

Protein

1u5b/bfactors	1u5b/average	bfactors/average
RMSD: 0.377	RMSD: 1.169	RMSD: 1.422

C-alpha

1u5b/bfactors	1u5b/average	bfactors/average
RMSD: 0.300	RMSD: 0.955	RMSD: 0.993

Radius of gyration

Structural analysis

First we had to use the command
trjconv -f wtMD.xtc -o wtMD_nojump.xtc -pbc nojump

Hydrogen bonds

echo 1 1 | g_hbond -f wtMD_nojump.xtc -s wtMD.tpr -num hydrogen-bonds-intra-protein.xvg
echo 1 12 | g_hbond -f wtMD_nojump.xtc -s wtMD.tpr -num hydrogen-bonds-protein-water.xvg

protein and protein	protein and water

Ramachandran plot

Analysis of dynamics and time-averaged properties

RMSD matrix

cluster analysis

internal RMSD