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MD simulation analysis TSD - Revision history
2024-03-29T15:59:30Z
Revision history for this page on the wiki
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https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28602&oldid=prev
Reeb: /* Conclusion */
2012-08-31T20:20:00Z
<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 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 observation of very limited flexibility is common throughout the molecular dynamics analysis. Although the structure vibrates and has some motile loops, one of which was also identified in NMA already, the quality assessment and further analyses leave doubts about whether the motions of the analysed protein domain can be regarded significant. Throughout the several analyses performed on the simulations, it stands out how little the simulations vary within and also between one and another as there is neither a significant difference between wildtype and mutation nor do the amino acid changes result in any major modifications. One can argue that this is not the point of an MD analysis, and naturally even small changes can have a large impact, however there is hardly anything in the simulations that seems to suggest disturbances of function or explain the enzymatic mechanism. In fact, it is questionable whether few changes might have been observed at all, had they not been known to happen before hand. That includes, that the rigidity of R178H seems to somehow suggest a loss in function, however at the same time the high flexibility of P182L can be considered an equally strong point for loss of function and as it is known from the previous analyses only the former mutation is actually disease causing. Unfortunately none of the simulations gave strong indications as to why this is. <del class="diffchange diffchange-inline">This</del> might be attributed to the fact that the MD analysis could have been performed in much more detail but the fact the first domain is missing, which seemed important <del class="diffchange diffchange-inline">according to</del> NMA, might have an equally large effect. In addition it should be remembered that the protein in question appears as a heterodimer and association between the alpha- and beta-subunit is essential for enzymatic activity.</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>The observation of very limited flexibility is common throughout the molecular dynamics analysis. Although the structure vibrates and has some motile loops, one of which was also identified in NMA already, the quality assessment and further analyses leave doubts about whether the motions of the analysed protein domain can be regarded significant. Throughout the several analyses performed on the simulations, it stands out how little the simulations vary within and also between one and another as there is neither a significant difference between wildtype and mutation nor do the amino acid changes result in any major modifications. One can argue that this is not the point of an MD analysis, and naturally even small changes can have a large impact, however there is hardly anything in the simulations that seems to suggest disturbances of function or explain the enzymatic mechanism. In fact, it is questionable whether few changes might have been observed at all, had they not been known to happen before hand. That includes, that the rigidity of R178H seems to somehow suggest a loss in function, however at the same time the high flexibility of P182L can be considered an equally strong point for loss of function and as it is known from the previous analyses only the former mutation is actually disease causing. Unfortunately none of the simulations gave strong indications as to why this is. <ins class="diffchange diffchange-inline">It</ins> might be attributed to the fact that the MD analysis could have been performed in much more detail but the fact<ins class="diffchange diffchange-inline"> that</ins> the first domain is missing,<ins class="diffchange diffchange-inline"> a domain</ins> which seemed important <ins class="diffchange diffchange-inline">during</ins> NMA, might have an equally large effect. In addition<ins class="diffchange diffchange-inline">,</ins> it should be remembered that the protein in question appears as a heterodimer and association between the alpha- and beta-subunit is essential for enzymatic activity.</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>=References=</div></td>
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Reeb
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28601&oldid=prev
Reeb: /* Flexibility */
2012-08-31T20:16:09Z
<p><span dir="auto"><span class="autocomment">Flexibility</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:16, 31 August 2012</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> in manual! (probably different)--></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><del class="diffchange diffchange-inline">=</del>==RMSD<del class="diffchange diffchange-inline">=</del>==</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>==RMSD==</div></td>
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Reeb
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28598&oldid=prev
Meiera: /* Ramachandran plots */
2012-08-31T20:12:03Z
<p><span dir="auto"><span class="autocomment">Ramachandran plots</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:12, 31 August 2012</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>| align="right" | [[Image:TSD_Rama_P182L.png|thumb|300px|P182L]]</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>
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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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <del class="diffchange diffchange-inline">TODO</del>: ''' Ramachandran plots for all 3 simulations. Displayed are angles for all amino acids but only from every 100th step.</div></font></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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <ins class="diffchange diffchange-inline">11</ins>: ''' Ramachandran plots for all 3 simulations. Displayed are angles for all amino acids but only from every 100th step.</div></font></div></td>
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Meiera
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28597&oldid=prev
Meiera: /* RMSD */
2012-08-31T20:11:48Z
<p><span dir="auto"><span class="autocomment">RMSD</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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <del class="diffchange diffchange-inline">TODO</del>: ''' Displayed is the RMSD from the backbone against the start structure.</div></font></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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <ins class="diffchange diffchange-inline">10</ins>: ''' Displayed is the RMSD from the backbone against the start structure.</div></font></div></td>
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Meiera
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28596&oldid=prev
Meiera: /* RMS Fluctuation plots */
2012-08-31T20:11:34Z
<p><span dir="auto"><span class="autocomment">RMS Fluctuation plots</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>| align="right" | [[Image:TSD 182L.prot.rmsf.xvg.eps.png|thumb|300px|P182L]]</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>| align="right" | [[Image:TSD 182L.prot.rmsf.xvg.eps.png|thumb|300px|P182L]]</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;"><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>
</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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <del class="diffchange diffchange-inline">TODO</del>: RMS fluctuation for every residue'''. According to previous results, only values calculated on all atoms are shown.</div></font></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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <ins class="diffchange diffchange-inline">9</ins>: RMS fluctuation for every residue'''. According to previous results, only values calculated on all atoms are shown.</div></font></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;"><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>
</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></figtable></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></figtable></div></td>
</tr>
</table>
Meiera
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28595&oldid=prev
Meiera: /* B-Factors */
2012-08-31T20:11:20Z
<p><span dir="auto"><span class="autocomment">B-Factors</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 20:11, 31 August 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 154:</td>
<td colspan="2" class="diff-lineno">Line 154:</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>| align="right" | [[Image:TSD MD 182L BF CA VS PROT.png|thumb|300px|P182L]]</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>| align="right" | [[Image:TSD MD 182L BF CA VS PROT.png|thumb|300px|P182L]]</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;"><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>
</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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <del class="diffchange diffchange-inline">TODO</del>: Comparison of B-Factors''' . Shown are the B-factors from converted RMSF values, using C-alpha only (dots) and all atoms (cartoon). Text in magenta denotes the amino acid at the two mutation positions as well was the B-factor value.</div></font></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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <ins class="diffchange diffchange-inline">8</ins>: Comparison of B-Factors''' . Shown are the B-factors from converted RMSF values, using C-alpha only (dots) and all atoms (cartoon). Text in magenta denotes the amino acid at the two mutation positions as well was the B-factor value.</div></font></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;"><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>
</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></figtable></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></figtable></div></td>
</tr>
</table>
Meiera
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28594&oldid=prev
Meiera: /* Radius of Gyration */
2012-08-31T20:11:06Z
<p><span dir="auto"><span class="autocomment">Radius of Gyration</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 20:11, 31 August 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 135:</td>
<td colspan="2" class="diff-lineno">Line 135:</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>| align="right" | [[Image:TSD 182L.prot.gyration.xvg.eps.png|thumb|300px|P182L]]</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>| align="right" | [[Image:TSD 182L.prot.gyration.xvg.eps.png|thumb|300px|P182L]]</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;"><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>
</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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <del class="diffchange diffchange-inline">TODO</del>: Gyration radii'''. Shown is the gyration radius and its component for every simulation. The calculations were performed on all atoms. </div></font></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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <ins class="diffchange diffchange-inline">7</ins>: Gyration radii'''. Shown is the gyration radius and its component for every simulation. The calculations were performed on all atoms. </div></font></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;"><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>
</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></figtable></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></figtable></div></td>
</tr>
</table>
Meiera
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28593&oldid=prev
Meiera: /* Total Energy */
2012-08-31T20:10:55Z
<p><span dir="auto"><span class="autocomment">Total Energy</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 20:10, 31 August 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 117:</td>
<td colspan="2" class="diff-lineno">Line 117:</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>| align="right" | [[Image:TSD 182L.totalEnergy.xvg.eps.png|thumb|300px|P182L, Average: -725500]]</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>| align="right" | [[Image:TSD 182L.totalEnergy.xvg.eps.png|thumb|300px|P182L, Average: -725500]]</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;"><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>
</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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <del class="diffchange diffchange-inline">TODO</del>: Total energy change during simulations.''' A cumulative average is shown in red. </div></font></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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <ins class="diffchange diffchange-inline">6</ins>: Total energy change during simulations.''' A cumulative average is shown in red. </div></font></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;"><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>
</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></figtable></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></figtable></div></td>
</tr>
</table>
Meiera
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28592&oldid=prev
Meiera: /* Potential Energy */
2012-08-31T20:10:42Z
<p><span dir="auto"><span class="autocomment">Potential Energy</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 20:10, 31 August 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 100:</td>
<td colspan="2" class="diff-lineno">Line 100:</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>| align="right" | [[Image:TSD 182L.potential.xvg.eps.png|thumb|300px|P182L Average: -884400]]</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>| align="right" | [[Image:TSD 182L.potential.xvg.eps.png|thumb|300px|P182L Average: -884400]]</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;"><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>
</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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <del class="diffchange diffchange-inline">TODO</del>: Potential energy changes during the simulations'''. A cumulative average is shown in red.</div></font></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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <ins class="diffchange diffchange-inline">5</ins>: Potential energy changes during the simulations'''. A cumulative average is shown in red.</div></font></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;"><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>
</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></figtable></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></figtable></div></td>
</tr>
</table>
Meiera
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=MD_simulation_analysis_TSD&diff=28591&oldid=prev
Meiera: /* Temperature */
2012-08-31T20:10:30Z
<p><span dir="auto"><span class="autocomment">Temperature</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 20:10, 31 August 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 81:</td>
<td colspan="2" class="diff-lineno">Line 81:</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>| align="right" | [[Image:TSD 182L.temperature.xvg.eps.png|thumb|300px|P182L Average: 297.9]]</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>| align="right" | [[Image:TSD 182L.temperature.xvg.eps.png|thumb|300px|P182L Average: 297.9]]</div></td>
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<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>|-</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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<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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <del class="diffchange diffchange-inline">TODO</del>: Temperature changes during the simulations.''' A cumulative average is shown in red.</div></font></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>|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table <ins class="diffchange diffchange-inline">4</ins>: Temperature changes during the simulations.''' A cumulative average is shown in red.</div></font></div></td>
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<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>|}</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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<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></figtable></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></figtable></div></td>
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</table>
Meiera