https://wiki.bwhpc.de/wiki/index.php?action=history&feed=atom&title=JUSTUS2%2FSoftware%2FNAMD 2026-10-28T12:53:45Z Revision history for this page on the wiki MediaWiki 1.39.17 https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=16436&oldid=prev 2026-09-22T09:32:15Z

<p><span dir="auto"><span class="autocomment">Example Scripts =</span></span></p> <table style="background-color: #fff; color: #202122;" 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: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:32, 22 September 2026</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 131:</td> <td colspan="2" class="diff-lineno">Line 131:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; 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>= Example Scripts <del style="font-weight: bold; text-decoration: none;">=</del>=</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>= Example Scripts =</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;syntaxhighlight lang="bash"&gt;</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;syntaxhighlight lang="bash"&gt;</div></td> </tr> </table>

K Siegmund https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=16435&oldid=prev 2026-09-22T09:31:21Z

<p>Auto-sync: Example Scripts</p> <table style="background-color: #fff; color: #202122;" 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: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:31, 22 September 2026</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 131:</td> <td colspan="2" class="diff-lineno">Line 131:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; 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 style="font-weight: bold; text-decoration: none;">=</del>= Example Scripts ==</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>= Example Scripts ==</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>&lt;syntaxhighlight lang="bash"&gt;</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#!/bin/bash</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># Allocate two nodes</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#SBATCH --nodes=2</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># Number of program instances to be executed</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#SBATCH --tasks-per-node=48</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># Allocate 20 (of 192) GB memory per node</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#SBATCH --mem=20gb</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># Maximum run time of job</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#SBATCH --time=00:10:00</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># Give job a reasonable name</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#SBATCH --job-name=bwhpc-example</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># File name for stdout/stderr (%j will be replaced by job id)</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#SBATCH --output=bwhpc-example_ID-%j.out</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#########################</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># bwHPC examples illustrate how to submit a batch job to the cluster queuing system. It is necessary to adapt certain specifications for your particular case.</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># General Hints</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># Parallel Execution:</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># It is usually more efficient to run several smaller jobs with reasonable speedup simultaneously. Check for a reasonable speedup by gradually increasing the number of workers from 1 or 2 to n cores. Do not forget to adjust the memory specification when changing the number of workers. Use $ seff &lt;jobid&gt; to get efficiency information.</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># Memory Management:</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># It requires some experience to choose the perfect memory value. Monitoring a job interactively may help to estimate the memory consumption. Requesting 1GB more than the required amount is typically sufficient. Use $ seff &lt;jobid&gt; to get efficiency information.</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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># Runtime Specification:</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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 wall-time limit is independent of the number of parallel workers. In general, jobs with shorter wall times get higher priorities. It could help to run the job interactively for a small period of time to monitor its convergence. Furthermore, it may be advantageous to extrapolate the run time by looking at smaller test jobs first.</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>#########################</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>module purge</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>module load chem/namd/2.14</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>module list</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>srun namd2 +isomalloc_sync apoa1.namd</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>exit 0</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>&lt;/syntaxhighlight&gt;</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>= Useful links =</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>= Useful links =</div></td> </tr> </table>

K Siegmund https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=16434&oldid=prev 2026-09-22T07:59:39Z

<p></p> <table style="background-color: #fff; color: #202122;" 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: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:59, 22 September 2026</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 130:</td> <td colspan="2" class="diff-lineno">Line 130:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>$ ls # when job finishes the results will be visible in this directory</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>$ ls # when job finishes the results will be visible in this directory</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>== Example Scripts ==</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>= Useful links =</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>= Useful links =</div></td> </tr> </table>

K Siegmund https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=12701&oldid=prev 2024-04-23T08:01:05Z

<p></p> <table style="background-color: #fff; color: #202122;" 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: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:01, 23 April 2024</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 137:</td> <td colspan="2" class="diff-lineno">Line 137:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>* [https://en.wikipedia.org/wiki/NAMD Wikipedia article (english)]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>* [https://en.wikipedia.org/wiki/NAMD Wikipedia article (english)]</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>* [https://de.wikipedia.org/wiki/NAMD Wikipedia article (german)]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>* [https://de.wikipedia.org/wiki/NAMD Wikipedia article (german)]</div></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; 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>----</div></td> <td colspan="2" class="diff-empty diff-side-added"></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; 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>[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div></td> <td colspan="2" class="diff-empty diff-side-added"></td> </tr> </table>

K Siegmund https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=11768&oldid=prev 2023-02-14T09:36:28Z

<p>K Siegmund moved page <a href="/e/NAMD" class="mw-redirect" title="NAMD">NAMD</a> to <a href="/e/JUSTUS2/Software/NAMD" title="JUSTUS2/Software/NAMD">JUSTUS2/Software/NAMD</a></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <tr class="diff-title" lang="en"> <td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:36, 14 February 2023</td> </tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div> </td></tr></table>

K Siegmund https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=11499&oldid=prev 2022-12-06T09:15:28Z

<p></p> <table style="background-color: #fff; color: #202122;" 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: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:15, 6 December 2022</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 9:</td> <td colspan="2" class="diff-lineno">Line 9:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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: #202122; 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>| Availability</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>| Availability</div></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; 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>| [[BwForCluster_JUSTUS_2]] &amp;#124; <del style="font-weight: bold; text-decoration: none;">[[BwForCluster_MLS&amp;WISO_Production]]</del></div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>| [[BwForCluster_JUSTUS_2]] &amp;#124; </div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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: #202122; 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>| License</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>| License</div></td> </tr> </table>

K Siegmund https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=11462&oldid=prev 2022-11-23T17:56:54Z

<p><span dir="auto"><span class="autocomment">Availability</span></span></p> <table style="background-color: #fff; color: #202122;" 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: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:56, 23 November 2022</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 30:</td> <td colspan="2" class="diff-lineno">Line 30:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>= Availability =</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>= Availability =</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; 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>NAMD is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from <del style="font-weight: bold; text-decoration: none;">the [</del>https://www.bwhpc.de/software.html <del style="font-weight: bold; text-decoration: none;">Cluster Information System (CIS)].</del></div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>NAMD is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from https://www.bwhpc.de/software.html </div></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; 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;"><br /></td> <td colspan="2" class="diff-empty diff-side-added"></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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 order to check which versions of NAMD are installed on the compute cluster, run the following command:</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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 order to check which versions of NAMD are installed on the compute cluster, run the following command:</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;pre&gt;</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;pre&gt;</div></td> </tr> </table>

K Siegmund https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=11280&oldid=prev 2022-11-01T11:20:32Z

<p></p> <table style="background-color: #fff; color: #202122;" 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: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:20, 1 November 2022</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 139:</td> <td colspan="2" class="diff-lineno">Line 139:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>* [https://de.wikipedia.org/wiki/NAMD Wikipedia article (german)]</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>* [https://de.wikipedia.org/wiki/NAMD Wikipedia article (german)]</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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" data-marker="−"></td> <td style="color: #202122; 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>[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2<del style="font-weight: bold; text-decoration: none;">]][[Category:BwForCluster_MLS&amp;WISO_Production</del>]]</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div></td> </tr> </table>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=9913&oldid=prev 2022-02-06T01:39:56Z

<p><span dir="auto"><span class="autocomment">Examples</span></span></p> <table style="background-color: #fff; color: #202122;" 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: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:39, 6 February 2022</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 119:</td> <td colspan="2" class="diff-lineno">Line 119:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; 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>Run a first simple example job on &lt;font color=red&gt;JUSTUS 2&lt;/font&gt;<del style="font-weight: bold; text-decoration: none;">.</del></div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>Run a first simple example job on &lt;font color=red&gt;JUSTUS 2&lt;/font&gt;<ins style="font-weight: bold; text-decoration: none;">:</ins></div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;pre&gt;</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;pre&gt;</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>$ module load chem/namd # load module</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>$ module load chem/namd # load module</div></td> </tr> </table>

F Wagner https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/NAMD&diff=9912&oldid=prev 2022-02-06T01:39:23Z

<p><span dir="auto"><span class="autocomment">Examples</span></span></p> <table style="background-color: #fff; color: #202122;" 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: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:39, 6 February 2022</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 119:</td> <td colspan="2" class="diff-lineno">Line 119:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;/pre&gt;</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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;"><br /></td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; 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>Run a first simple example job<del style="font-weight: bold; text-decoration: none;">:</del></div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; 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>Run a first simple example job<ins style="font-weight: bold; text-decoration: none;"> on &lt;font color=red&gt;JUSTUS 2&lt;/font&gt;.</ins></div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;pre&gt;</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>&lt;pre&gt;</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>$ module load chem/namd # load module</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; 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>$ module load chem/namd # load module</div></td> </tr> </table>

F Wagner