<br><div><br></div><div>Hi </div><div><br></div><div>From source code => gmx_rmsf.c </div><div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; color: #891315">"g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard "<span style="color: #000000">,</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; color: #891315"><span style="color: #000000"> </span>"deviation) of atomic positions "<span style="color: #000000">,</span></p>
<br class="Apple-interchange-newline"></div><div><br></div><div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"> <span style="color: #760f50">if</span> (devfn) {</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; color: #236e25"><span style="color: #000000"> </span>/* Calculate RMS Deviation */</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"> <span style="color: #760f50">for</span>(i=<span style="color: #0000ff">0</span>;(i<isize);i++) {</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-tab-span" style="white-space:pre"> </span>aid = index[i];</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-tab-span" style="white-space:pre"> </span><span style="color: #760f50">for</span>(d=<span style="color: #0000ff">0</span>;(d<DIM);d++) {</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-tab-span" style="white-space:pre"> </span> rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-tab-span" style="white-space:pre"> </span>}</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"> }</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"> } </p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"> count += <span style="color: #0000ff">1.0</span>;</p>
<br class="Apple-interchange-newline"></div><div><br></div><div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco">rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;</p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco">
<br></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><br></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">Therefore, g_rmsf is the average of structure deviation over the time frames.</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">However, I issued the commands ( C-alpha is selected )</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 0 -e 100 -s abc-crystal.tpr -o RMSF-abc-0th-100th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco">
<span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 100 -e 200 -s abc-crystal.tpr -o RMSF-abc-100th-200th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 200 -e 300 -s abc-crystal.tpr -o RMSF-abc-200th-300th.xvg</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 300 -e 400 -s abc-crystal.tpr -o RMSF-abc-300th-400th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco">
<span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 400 -e 500 -s abc-crystal.tpr -o RMSF-abc-400th-500th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 500 -e 600 -s abc-crystal.tpr -o RMSF-abc-500th-600th.xvg</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 600 -e 700 -s abc-crystal.tpr -o RMSF-abc-600th-700th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco">
<span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 700 -e 800 -s abc-crystal.tpr -o RMSF-abc-700th-800th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 800 -e 900 -s abc-crystal.tpr -o RMSF-abc-800th-900th.xvg</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 900 -e 1000 -s abc-crystal.tpr -o RMSF-abc-900th-1000th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco">
<span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco">
<span class="Apple-style-span" style="font-size: small;">Also, ( C-alpha is selected )</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">g_rmsf -f abc.xtc -b 0 -e 1000 -s abc-crystal.tpr -o RMSF-abc-0th-1000th.xvg</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br>
</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">Then I ploted, </span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-0th-100th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-100th-200th.xvg</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-200th-300th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-300th-400th.xvg</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-400th-500th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-500th-600th.xvg</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-600th-700th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-700th-800th.xvg</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-800th-900th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">RMSF-abc-900th-1000th.xvg</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br>
</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">Also, I ploted</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco">
<span class="Apple-style-span" style="font-size: small;">RMSF-abc-0th-1000th.xvg</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br>
</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">The PLOT RMSF-abc-0th-1000th.xvg has all RMSF-Values much higher than those from RMSF-abc-0th-100th.xvg / RMSF-abc-100th-200th.xvg / RMSF-abc-200th-300th.xvg / ...... / RMSF-abc-900th-1000th.xvg.......</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br>
</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">It does not make sense... I supposed.....</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco">
<span class="Apple-style-span" style="font-size: small;">Did I misunderstand something ?</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br>
</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br>
</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">THank you</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;">Lin</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br>
</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco"><span class="Apple-style-span" style="font-size: small;"><br>
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