Difference between revisions of "MD Mutation436"
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=== Visualize in pymol === |
=== Visualize in pymol === |
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| + | First of all, we visualized the simulation with with ngmx, because it draws bonds based on the topology file. ngmx gave the user the possibility to choose different parameters. Therefore, we decided to visualize the system with following parameters: |
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| + | {| border="1" style="text-align:center; border-spacing:0;" |
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| + | |Group 1 |
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| + | |Group 2 |
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| + | |- |
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| + | |System |
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| + | |Water |
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| + | |- |
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| + | |Protein |
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| + | |Ion |
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| + | |- |
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| + | |Backbone |
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| + | |NA |
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| + | |- |
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| + | |MainChain+H |
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| + | |CL |
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| + | |- |
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| + | |SideChain |
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| + | | |
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| + | |- |
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| + | |} |
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| + | |||
| + | Here is a picture of the visualization with ngmx: |
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| + | |||
| + | | [[Image:ngmx_mut436.png|thumb|Visualisation of the MD simulation for Mutation 436]] |
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=== create a movie === |
=== create a movie === |
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Revision as of 10:13, 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.
Visualize in pymol
First of all, we visualized the simulation with with ngmx, because it draws bonds based on the topology file. ngmx gave the user the possibility to choose different parameters. Therefore, we decided to visualize the system with following parameters:
| Group 1 | Group 2 |
| System | Water |
| Protein | Ion |
| Backbone | NA |
| MainChain+H | CL |
| SideChain |
Here is a picture of the visualization with ngmx:
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