Difference between revisions of "Molecular Dynamics Analysis BCKDHA"
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=== Solvent accessible surface area === |
=== Solvent accessible surface area === |
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+ | !Solvent accessible surface |
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+ | !SAS over time per residue |
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+ | !SAS over time per atom |
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+ | |- |
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+ | |[[File:Solvent-accessible-surface_MD_BCKDHA.png|thumb|300px]] |
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+ | || [[File:Residue-sas_MD_BCKDHA.png|thumb|300px]] || |
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+ | [[File:Atomic-sas_MD_BCKDHA.png|thumb|300px]] |
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+ | |} |
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=== Hydrogen bonds === |
=== Hydrogen bonds === |
Revision as of 10:29, 5 September 2011
Contents
- 1 A brief check of results
- 1.1 How many frames are in the trajectory file and what is the time resolution?
- 1.2 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?
- 1.3 Which contribution to the potential energy accounts for most of the calculations?
- 2 Visualization of results
- 3 Quality assurance
- 4 Structural analysis
- 5 Analysis of dynamics and time-averaged properties
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
|
Temperature
|
Potential
|
Total Energy
|
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
Solvent accessible surface area
Solvent accessible surface | SAS over time per residue | SAS over time per atom |
---|---|---|
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 |
---|---|