MD WildeType
From Bioinformatikpedia
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.