Difference between revisions of "Molecular Dynamics Analysis BCKDHA"

From Bioinformatikpedia
(Solvent accessible surface area)
(Pymol analysis of average and bfactor)
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=== Pymol analysis of average and bfactor ===
 
=== Pymol analysis of average and bfactor ===
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To analyze the average and the bfactor we used pymol.
   
 
==== Protein ====
 
==== Protein ====

Revision as of 10:32, 5 September 2011

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

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

Temperature

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

Potential

align="center"
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.

Minimal periodic distance BCKDHA MD.png

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 per residue protein MD BCKDHA.png

RMSF for C-alpha

Rmsf per residue ca MD BCKDHA.png

Pymol analysis of average and bfactor

To analyze the average and the bfactor we used pymol.

Protein

1u5b/bfactors 1u5b/average bfactors/average
Bckdha bfactors MD BCKDHA.png
Bckdha average MD BCKDHA.png
Pymol rmsf protein bfactors BCKDHA.png
RMSD: 0.377 RMSD: 1.169 RMSD: 1.422

C-alpha

1u5b/bfactors 1u5b/average bfactors/average
Bckdha bfactors ca MD BCKDHA.png
Bckdha average ca MD BCKDHA.png
Pymol rmsf calpha bfactors BCKDHA new.png
RMSD: 0.300 RMSD: 0.955 RMSD: 0.993

Radius of gyration

Radius off gyration MD BCKDHA.png

Structural analysis

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

Solvent accessible surface area

Solvent accessible surface SAS over time per residue SAS over time per atom
Solvent-accessible-surface MD BCKDHA.png
Residue-sas MD BCKDHA.png
Atomic-sas MD BCKDHA.png

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
Hydrogen bonds intra protein MD BCKDHA.png
Hydrogen-bonds-protein-water MD BCKDHA.png

salt bridges

Ramachandran plot

Ramachandran plot MD BCKDHA.png

Analysis of dynamics and time-averaged properties

RMSD matrix

Rmsd-matrix MD BCKDHA.jpg

cluster analysis

Cluster MD BCKDHA.png
Rmsd-distribution MD BCKDHA.png

internal RMSD

Distance-rmsd MD BCKDHA.png