Difference between revisions of "MD Mutation436"
From Bioinformatikpedia
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gmxcheck -f mut436_md.xtc |
gmxcheck -f mut436_md.xtc |
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With the command we got following results: |
With the command we got following results: |
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Revision as of 10:00, 29 August 2011
Contents
- 1 check the trajectory
- 2 Visualize in pymol
- 3 create a movie
- 4 energy calculations for pressure, temperature, potential and total energy
- 5 minimum distance between periodic boundary cells
- 6 RMSF for protein and C-alpha
- 7 Pymol analysis of average and bfactor
- 8 Radius of gyration
- 9 solvent accesible surface area
- 10 hydrogen-bonds
- 11 salt bridges
- 12 Ramachandran plot
- 13 RMSD matrix
- 14 cluster analysis
- 15 internal RMSD
check the trajectory
We checked the trajectory with following command:
gmxcheck -f mut436_md.xtc
With the command we got following results:
Reading frame 0 time 0.000 # Atoms 96555 Precision 0.001 (nm) Last frame 2000 time 10000.000
Furthermore, we got some detailed results about the different items during the simulation.
| Item | #frames | Timestep (ps) |
| Step | 2001 | 5 |
| Time | 2001 | 5 |
| Lambda | 0 | - |
| Coords | 2001 | 5 |
| Velocities | 0 | - |
| Forces | 0 | - |
| Box | 2001 | 5 |
The simulation finished on node 0 Fri Aug 26 08:40:07 2011.
| Time | ||
| Node (s) | Real (s) | % |
| 34860.474 | 34860.474 | 100% |
| 9h41:00 | ||
The complete simulation needs 9 hours and 41 minutes to finishing.
| Performance | |||
| Mnbf/s | GFlops | ns/day | hour/ns |
| 818.560 | 60.105 | 24.785 | 0.968 |
As you can see in the table above, it takes about 1 hour to simulat 1ns of the system. So therefore, it would be possible to simulate about 25ns in one complete day calculation time.
