Molecular Dynamics Analysis BCKDHA

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Revision as of 14:00, 4 September 2011 by Reisinger (talk | contribs) (C-alpha)

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

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

Temperature

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

Potential

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

Total Energy

Energy MD BCKDHA.png
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.

align="center"

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

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RMSF for C-alpha

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Pymol analysis of average and bfactor

Protein

bfactors/average
Pymol rmsf protein bfactors BCKDHA.png

C-alpha

bfactors/average
Pymol rmsf calpha bfactors BCKDHA.png

Radius of gyration

Structural analysis

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

Solvent accessible surface area

Hydrogen bonds

protein and protein

protein and water

salt bridges

Ramachandran plot

Analysis of dynamics and time-averaged properties

RMSD matrix

cluster analysis

internal RMSD