Difference between revisions of "MD WildeType"

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=== 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.
 
 
{| border="1" style="text-align:center; border-spacing:0;"
 
|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
 
 
{| border="1" style="text-align:center; border-spacing:0;"
 
|colspan="3" | Time
 
|-
 
|Node (s)
 
|Real (s)
 
|%
 
|-
 
|22438.875
 
|22438.875
 
|1oo%
 
|-
 
|colspan="3" | 6h13:58
 
|-
 
|}
 
 
The complete simulation needs 6 hours and 13 minutes to finishing.
 
{| border="1" style="text-align:center; border-spacing:0;"
 
|colspan="4" | 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:
 
 
{| border="1" style="text-align:center; border-spacing:0;"
 
|Group 1
 
|Group 2
 
|-
 
|System
 
|Water
 
|-
 
|Protein
 
|Ion
 
|-
 
|Backbone
 
|NA
 
|-
 
|MainChain+H
 
|CL
 
|-
 
|SideChain
 
|
 
|-
 
|}
 
 
Figure 1 shows the visualization with ngmx:
 
 
[[Image:ngmx_mut436.png|thumb|center|Figure 1: Visualisation of the MD simulation for Mutation 436 with ngmx]]
 
 
Next, we want to visualize the protein with pymol. Therefore, we extracted 1000 frames from the trajectory, leaving out the water and jump over the boundaries to make continuse trajectories. Therefore, we used following command:
 
 
trjconv -s fole.tpr -f file.xtc -o output_file.pdb -pbc nojump -dt 10
 
 
The program asks for the a group as output. We want to see the whole system, therefore we decided to use group 0.
 

Latest revision as of 09:37, 19 September 2011