Difference between revisions of "MD Mutation436"

From Bioinformatikpedia
(→‎check the trajectory)
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=== check the trajectory ===
  
=== check the trajectory ===
  +
  +
We checked the trajectory with following command:
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  +
gmxcheck -f mut436_md.xtc
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  +
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.
  +
  +
{| border="1" style="text-align:center; border-spacing:0;"
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|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.
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  +
{| border="1" style="text-align:center; border-spacing:0;"
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|colspan="4" | Time
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|-
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|Node (s)
  +
|Real (s)
  +
|%
  +
|rowspan="2" |
  +
|-
  +
|34860.474
  +
|34860.474
  +
|100%
  +
|-
  +
|colspan="4" | 9h41:00
  +
|-
  +
|colspan="4" | Performance
  +
|-
  +
|Mnbf/s
  +
|GFlops
  +
|ns/day
  +
|hour/ns
  +
|-
  +
|818.560
  +
|60.105
  +
|24.785
  +
|0.968
  +
|-
  +
|}
   
 
=== Visualize in pymol ===
  
=== Visualize in pymol ===

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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