MD Mutation436

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Revision as of 10:42, 29 August 2011 by Link (talk | contribs) (Visualize in pymol)

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:

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.

create a movie

energy calculations for pressure, temperature, potential and total energy

minimum distance between periodic boundary cells

RMSF for protein and C-alpha

Pymol analysis of average and bfactor

Radius of gyration

solvent accesible surface area

hydrogen-bonds

salt bridges

Ramachandran plot

RMSD matrix

cluster analysis

internal RMSD