Difference between revisions of "MD Mutation436"

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(→‎check the trajectory)
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Revision as of 09:57, 29 August 2011

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
Performance
Mnbf/s GFlops ns/day hour/ns
818.560 60.105 24.785 0.968

Visualize in pymol

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

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