# Difference between revisions of "Normal mode analysis HEXA"

From Bioinformatikpedia

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=== Results === |
=== Results === |
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+ | We took the first five models (7, 8, 9, 10, 11). |
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+ | Here you can see the normalized squared atomic displacments of our models: |
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+ | {| border="1" style="text-align:center; border-spacing:0;" |
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+ | |model 7 |
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+ | |model 8 |
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+ | |model 9 |
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+ | |model 10 |
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+ | |model 11 |
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+ | |- |
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+ | |[[Image:mode_1_plot.png|thumb|150px|...]] |
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+ | |[[Image:mode_2_plot.png|thumb|150px|...]] |
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+ | |[[Image:mode_3_plot.png|thumb|150px|...]] |
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+ | |[[Image:mode_4_plot.png|thumb|150px|...]] |
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+ | |[[Image:mode_5_plot.png|thumb|150px|...]] |
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+ | |- |
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+ | |} |
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+ | |||

+ | |||

+ | Here you can see the motion of our analyses. |
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+ | |||

+ | {| border="1" style="text-align:center; border-spacing:0;" |
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+ | |model 7 |
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+ | |model 8 |
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+ | |model 9 |
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+ | |model 10 |
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+ | |model 11 |
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+ | |- |
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+ | |[[Image:model7.gif|thumb|150px|normalized squared atomic displacments of model 7]] |
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+ | |[[Image:webnma_model8.gif|thumb|150px|normalized squared atomic displacments of model 8]] |
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+ | |[[Image:webnma_model9.gif|thumb|150px|normalized squared atomic displacments of model 9]] |
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+ | |[[Image:webnma_model10.gif|thumb|150px|normalized squared atomic displacments of model 10]] |
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+ | |[[Image:webnma_model11.gif|thumb|150px|normalized squared atomic displacments of model 11]] |
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+ | |- |
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+ | |} |
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== All-atom NMA using Gromacs on the NOMAD-Ref server == |
== All-atom NMA using Gromacs on the NOMAD-Ref server == |

## Revision as of 12:40, 14 July 2011

## Contents

## Webnma

#### General information

#### Results

We analysed the five models with the lowest energy values. Webnma calculates fourteen different models with following energy values:

Mode Index | Deformation Energy |

7 | 1041.88 |

8 | 1318.21 |

9 | 1738.30 |

10 | 2841.31 |

11 | 3135.09 |

12 | 4100.18 |

13 | 3911.06 |

14 | 5337.50 |

15 | 5741.69 |

16 | 6513.85 |

17 | 6081.05 |

18 | 6882.96 |

19 | 7514.14 |

20 | 7943.67 |

We took the first five models (7, 8, 9, 10, 11).

Here you can see the normalized squared atomic displacments of our models:

model 7 | model 8 | model 9 | model 10 | model 11 |

Here you can see the motion of our analyses.

model 7 | model 8 | model 9 | model 10 | model 11 |

## NOMAD-Ref

### General information

### Results

We took the first five models (7, 8, 9, 10, 11).

Here you can see the normalized squared atomic displacments of our models:

model 7 | model 8 | model 9 | model 10 | model 11 |

Here you can see the motion of our analyses.

model 7 | model 8 | model 9 | model 10 | model 11 |