Difference between revisions of "MD WildeType"

From Bioinformatikpedia
(check the trajectory)
(Visualize in pymol)
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Figure 1 shows the visualization with ngmx:
 
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]]
+
[[Image:ngmx_2GJX.png|thumb|center|Figure 1: Visualisation of the MD simulation for the wildtype 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:
+
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 continouse trajectories. Therefore, we used following command:
   
 
trjconv -s fole.tpr -f file.xtc -o output_file.pdb -pbc nojump -dt 10
 
trjconv -s fole.tpr -f file.xtc -o output_file.pdb -pbc nojump -dt 10

Revision as of 09:12, 19 September 2011

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:

Figure 1: Visualisation of the MD simulation for the wildtype 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 continouse 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.