https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&feed=atom&action=history
Molecular Dynamics Analysis GLA - Revision history
2024-03-29T04:41:46Z
Revision history for this page on the wiki
MediaWiki 1.31.16
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15979&oldid=prev
Grandke: /* Visualization of the results */
2011-10-25T00:38:41Z
<p><span dir="auto"><span class="autocomment">Visualization of the results</span></span></p>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Figures 1,2 ,and 3 show every <del class="diffchange diffchange-inline">~30</del> frame of the molecular dynamics simulation. An animated figure of all 1000 simulated frames would be to large for this wiki. All animations show similar but not identical movement of the protein.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Figures 1,2 ,and 3 show<ins class="diffchange diffchange-inline"> about</ins> every <ins class="diffchange diffchange-inline">thirtieths</ins> frame of the molecular dynamics simulation. An animated figure of all 1000 simulated frames would be to large for this wiki. All animations show similar but not identical movement of the protein.</div></td>
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Grandke
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15978&oldid=prev
Grandke: /* Root mean square deviations again */
2011-10-25T00:35:55Z
<p><span dir="auto"><span class="autocomment">Root mean square deviations again</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Figures 53, 54 and 55 show the RMSD matrix for the proteins. This time the results for the proteins are all different. The wildtype proteins matrix has a thin light blue diagonal, surrounded by a wider green one that fluently becomes yellow. There only very few red parts at the bottom right/top left border. The mutation 3 proteins matrix has almost no light blue and the diagonal is green instead. The areas surrounding the diagonal are mixed in green and yellow. There is one very significant area between 7000 and 8000 ps, where the area is almost completely red and yellow, except the area that is very close to the diagonal. In addition the top left/bottom right corner are yellow and red, as well. The mutation 8 proteins matrix also has no light blue, but a green diagonal.The top right corner is mostly colored green, with some yellow in it. The top left/bottom right quarters are yellow and red.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Figures 53, 54 and 55 show the RMSD matrix for the proteins. This time the results for the proteins are all different. The wildtype proteins matrix has a thin light blue diagonal, surrounded by a wider green one that fluently becomes yellow. There only very few red parts at the bottom right/top left border. The mutation 3 proteins matrix has almost no light blue and the diagonal is green instead. The areas surrounding the diagonal are mixed in green and yellow. There is one very significant area between 7000 and 8000 ps, where the area is almost completely red and yellow, except the area that is very close to the diagonal. In addition the top left/bottom right corner are yellow and red, as well. The mutation 8 proteins matrix also has no light blue, but a green diagonal.The top right corner is mostly colored green, with some yellow in it. The top left/bottom right quarters are yellow and red.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>As the coloring is very bright the results seem to differ a lot, but the overall patterns equal each other. Thus, the values differ slightly, but there is no significant change that could be interpreted as disease causing. Since the values of the color scheme are different the red parts values in the wildtype protein are even higher than the ones in the mutated proteins.</div></td>
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Grandke
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15977&oldid=prev
Grandke: /* Conclusion */
2011-10-25T00:26:10Z
<p><span dir="auto"><span class="autocomment">Conclusion</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Conclusion=</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Conclusion=</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Almost none of the analysis steps above show significant differences between the wildtype protein and the mutant proteins. The results are either identical or very similar, what makes an interpretation very difficult. There are no assumptions that can be made only on the basis of the molecular dynamics analysis. It is impossible to classify one of the mutations as disease causing or not. <del class="diffchange diffchange-inline">Previous</del> <del class="diffchange diffchange-inline">assumptions</del> can <del class="diffchange diffchange-inline">not</del> be confirmed, as well.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Almost none of the analysis steps above show significant differences between the wildtype protein and the mutant proteins. The results are either identical or very similar, what makes an interpretation very difficult. There are no assumptions that can be made only on the basis of the molecular dynamics analysis. It is impossible to classify one of the mutations as disease causing or not. <ins class="diffchange diffchange-inline">In</ins> <ins class="diffchange diffchange-inline">our report we made the assumption that the mutation 3 protein is very likely to cause Fabry disease, based on the structure based mutation analysis. This</ins> can <ins class="diffchange diffchange-inline">neither</ins> be confirmed<ins class="diffchange diffchange-inline"> nor denied. The mutated proteins results are very similar and as mutation 8 is known as disease causing, this can be interpreted as an evidence for mutation 3 is non-neutral. On the other hand the results are similar to the non-mutated wildtype protein</ins>, as well<ins class="diffchange diffchange-inline"> and thus can be interpreted as evidence for neutrality. The few difference are not strong enough to work as a basis for the argumentation that mutation 3 is disease causing. Without the a priori knowledge about mutation 8, we most probably would declare both mutations as neutral, because of their similarity to the wildtype protein</ins>.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= References =</div></td>
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Grandke
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15976&oldid=prev
Grandke: /* Total Energy */
2011-10-24T19:45:10Z
<p><span dir="auto"><span class="autocomment">Total Energy</span></span></p>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Figures 13,14 and 15 show the values of the total energy during the simulation. All diagrams show variation around a value of ~700,000 and there are no results that show a reasonable difference between the proteins.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Figures 13,14 and 15 show the values of the total energy during the simulation. All diagrams show variation around a value of ~700,000 and there are no results that show a reasonable difference between the proteins<ins class="diffchange diffchange-inline">. The range of the values is small so they seem to be converged</ins>.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Minimum distances between periodic images===</div></td>
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Grandke
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15975&oldid=prev
Grandke: /* Potential */
2011-10-24T19:43:21Z
<p><span dir="auto"><span class="autocomment">Potential</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Figures 10, 11 and 12 show the potential values during the simulation. <del class="diffchange diffchange-inline">Similar</del> to the pressure values, there are <del class="diffchange diffchange-inline">high</del> variations around <del class="diffchange diffchange-inline">a</del> value <del class="diffchange diffchange-inline">of </del>-853,000 and the simulations seem to have<del class="diffchange diffchange-inline"> not</del> reached <del class="diffchange diffchange-inline">the</del> <del class="diffchange diffchange-inline">certain</del> equilibria <del class="diffchange diffchange-inline">and there</del> is no <del class="diffchange diffchange-inline">obvious</del> difference between the wildtype protein and the mutated ones.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Figures 10, 11 and 12 show the potential values during the simulation. <ins class="diffchange diffchange-inline">In opposite</ins> to the pressure values, there are <ins class="diffchange diffchange-inline">only low</ins> variations around <ins class="diffchange diffchange-inline">one</ins> value <ins class="diffchange diffchange-inline">(</ins>-853,000<ins class="diffchange diffchange-inline">)</ins> and the simulations seem to have reached <ins class="diffchange diffchange-inline">their</ins> <ins class="diffchange diffchange-inline">particular</ins> equilibria<ins class="diffchange diffchange-inline">.</ins> <ins class="diffchange diffchange-inline">There</ins> is no <ins class="diffchange diffchange-inline">significant</ins> difference between the wildtype protein and the mutated ones<ins class="diffchange diffchange-inline">, so the impact of the mutations on the potential is vanishingly low</ins>.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>====Total Energy====</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>====Total Energy====</div></td>
</tr>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"</div></td>
</tr>
<!-- diff cache key wikidb:diff:wikidiff2:1.12:old-15974:rev-15975:1.7.3:0 -->
</table>
Grandke
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15974&oldid=prev
Grandke: /* Pressure */
2011-10-24T17:50:13Z
<p><span dir="auto"><span class="autocomment">Pressure</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:50, 24 October 2011</td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Figures 7, 8 and 9 show the pressure values during the simulation. All proteins have high levels of variation (>600 kJ/mol) and have averages around zero. The mutated proteins averages both are slightly negative, but in the circumstances of the high overall variation this seems not significant.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Figures 7, 8 and 9 show the pressure values during the simulation. All proteins have high levels of variation (>600 kJ/mol) and have averages around zero. The mutated proteins averages both are slightly negative, but in the circumstances of the high overall variation this seems not significant<ins class="diffchange diffchange-inline">. It is not expected that the values converge to a certain value</ins>.</div></td>
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<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>====Potential====</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>====Potential====</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"</div></td>
</tr>
</table>
Grandke
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15973&oldid=prev
Grandke: /* Introduction */
2011-10-24T17:48:08Z
<p><span dir="auto"><span class="autocomment">Introduction</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<col class="diff-marker" />
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:48, 24 October 2011</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Introduction=</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Introduction=</div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In this task we analysed the simulated data that have been created within task 8. We used several tools of GROMACS to analyse the data and Pymol to visualize them. As the single steps of this task were exactly done according to the [http://md.chem.rug.nl/~mdcourse/analysis1.html<del class="diffchange diffchange-inline">|</del> tutorial] from the[[Task_10_-_Molecular_Dynamics_Simulations| task 10 page]] there is no methods section provided on this page.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In this task we analysed the simulated data that have been created within task 8. We used several tools of GROMACS to analyse the data and Pymol to visualize them. As the single steps of this task were exactly done according to the [http://md.chem.rug.nl/~mdcourse/analysis1.html tutorial] from the[[Task_10_-_Molecular_Dynamics_Simulations| task 10 page]] there is no methods section provided on this page.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Results=</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Results=</div></td>
</tr>
</table>
Grandke
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15972&oldid=prev
Grandke: /* Temperature */
2011-10-24T17:47:47Z
<p><span dir="auto"><span class="autocomment">Temperature</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:47, 24 October 2011</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The mutated proteins (Figures 5 and 6) temperatures averages are slightly higher than the wildtype proteins (Figure 4) one, but there is no significant increase. The lowest temperature of the mutation 8 protein is even lower than the minimum of the wildtype. The general appearance of the temperature diagram differs between the proteins, but there is no change into a certain direction.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The mutated proteins (Figures 5 and 6) temperatures averages are slightly higher than the wildtype proteins (Figure 4) one, but there is no significant increase. The lowest temperature of the mutation 8 protein is even lower than the minimum of the wildtype. The general appearance of the temperature diagram differs between the proteins, but there is no change into a certain direction<ins class="diffchange diffchange-inline">. Thus, the mutations seem not to influence the temperature significantly. In all simulations the temperature varies within a very small range, and therefore could be declared as stabilized</ins>.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>====Pressure====</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>====Pressure====</div></td>
</tr>
</table>
Grandke
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15931&oldid=prev
Grandke: /* Introduction */
2011-10-20T15:59:58Z
<p><span dir="auto"><span class="autocomment">Introduction</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:59, 20 October 2011</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Introduction=</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Introduction=</div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In this task we analysed the simulated data that have been created within task 8. We used several tools of GROMACS to analyse the data and Pymol to visualize them. As the single steps of this task were exactly done according to the [http://md.chem.rug.nl/~mdcourse/analysis1.html| tutorial] from the[[Task_10_-_Molecular_Dynamics_Simulations| task 10 page]] there is no methods section <del class="diffchange diffchange-inline">in</del> this page.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In this task we analysed the simulated data that have been created within task 8. We used several tools of GROMACS to analyse the data and Pymol to visualize them. As the single steps of this task were exactly done according to the [http://md.chem.rug.nl/~mdcourse/analysis1.html| tutorial] from the[[Task_10_-_Molecular_Dynamics_Simulations| task 10 page]] there is no methods section <ins class="diffchange diffchange-inline">provided on</ins> this page.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Results=</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Results=</div></td>
</tr>
</table>
Grandke
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamics_Analysis_GLA&diff=15930&oldid=prev
Grandke: /* Introduction */
2011-10-20T15:59:36Z
<p><span dir="auto"><span class="autocomment">Introduction</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
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<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:59, 20 October 2011</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Introduction=</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Introduction=</div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In this task we analysed the simulated data that have been created within task 8. We used several tools of GROMACS to analyse the data and Pymol to visualize them. <del class="diffchange diffchange-inline">The</del> single steps were done according to the [http://md.chem.rug.nl/~mdcourse/analysis1.html| tutorial] from the[[Task_10_-_Molecular_Dynamics_Simulations| task 10 page]].</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In this task we analysed the simulated data that have been created within task 8. We used several tools of GROMACS to analyse the data and Pymol to visualize them. <ins class="diffchange diffchange-inline">As the</ins> single steps<ins class="diffchange diffchange-inline"> of this task</ins> were<ins class="diffchange diffchange-inline"> exactly</ins> done according to the [http://md.chem.rug.nl/~mdcourse/analysis1.html| tutorial] from the[[Task_10_-_Molecular_Dynamics_Simulations| task 10 page]]<ins class="diffchange diffchange-inline"> there is no methods section in this page</ins>.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Results=</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=Results=</div></td>
</tr>
</table>
Grandke