MD WildeType
check the trajectory
We checked the trajectory with following command:
gmxcheck -f 2GJX_A_md.xtc
With the command we got following results:
Reading frame 0 time 0.000 # Atoms 96543 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 Thu Sep 15 23:45:08 2011
| Time | ||
| Node (s) | Real (s) | % |
| 22438.875 | 22438.875 | 1oo% |
| 6h13:58 | ||
The complete simulation needs 6 hours and 13 minutes to finishing.
| Performance | |||
| Mnbf/s | GFlops | ns/day | hour/ns |
| 1271.745 | 93.383 | 38.505 | 0.623 |
As you can see in the table above, it takes about half an hour to simulate 1ns of the system. So therefore, it would be possible to simulate about 40ns 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 |
Figure 1 shows the visualization with ngmx:
