layout: post
title: gnuplot绘制RMSD的统计直方图
categories:
在进行蛋白的分子动力学模拟时, 经常需要查看RMSD, 看蛋白是否已经稳定. 计算RMSD的方法很简单, 直接gmx rms即可得到rmsd.xvg, 然后就可以进行作图. 在展示RMSD演化图时, 经常还会同时给出其统计直方图, 这样可以更直观地看出RMSD是否已经稳定. 下面记录使用gnuplot作统计直方图的几种方法备用.
统计分布
<table class="highlighttable"><th colspan="2" style="text-align:left">gnuplot</th><tr><td><div class="linenodiv" style="background-color: #f0f0f0; padding-right: 10px"><pre style="line-height:125%">1
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<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">table</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">output</span> <span style="color: #BB4444">'</span>freq<span style="color: #666666">.</span>dat<span style="color: #BB4444">'</span>
<span style="color: #AA22FF; font-weight: bold">plot</span> <span style="color: #BB4444">'</span>C<span style="color: #666666">:</span><span style="#FF0000">\</span>Users<span style="#FF0000">\</span>Jicun<span style="#FF0000">\</span>Desktop<span style="#FF0000">\</span>_JOB<span style="#FF0000">\</span><span style="color: #666666">1</span>y57<span style="#FF0000">\</span>rmsd<span style="color: #666666">.</span>xvg<span style="color: #BB4444">'</span> <span style="color: #AA22FF">u</span> (<span style="color: #AA22FF">bin</span>(<span style="#FF0000">$</span><span style="color: #666666">2,</span><span style="color: #AA22FF">w</span>))<span style="color: #666666">:</span>(<span style="color: #666666">1</span>) <span style="color: #AA22FF">s</span> f <span style="color: #AA22FF">w</span> p
<span style="color: #AA22FF; font-weight: bold">unset</span> <span style="color: #AA22FF">table</span>
</pre></div>
</td></tr></table>带误差的直方图
<table class="highlighttable"><th colspan="2" style="text-align:left">gnuplot</th><tr><td><div class="linenodiv" style="background-color: #f0f0f0; padding-right: 10px"><pre style="line-height:125%">1
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<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">style</span> data histograms
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">style</span> histogram errorbars gap <span style="color: #666666">0</span> lw <span style="color: #666666">2</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">style</span> fill solid <span style="color: #666666">1</span> border <span style="color: #666666">0</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">bar</span> <span style="color: #666666">2</span>
<span style="#FF0000">stat</span> <span style="#FF0000">'fre</span><span style="color: #AA22FF; font-weight: bold">q</span><span style="#FF0000">.dat'</span> <span style="#FF0000">u</span> <span style="#FF0000">2</span> <span style="#FF0000">nooutput</span>
<span style="color: #AA22FF; font-weight: bold">plot</span> [<span style="color: #666666">0:</span>] <span style="color: #BB4444">'</span>freq<span style="color: #666666">.</span>dat<span style="color: #BB4444">'</span> <span style="color: #AA22FF">using</span> (<span style="#FF0000">$</span><span style="color: #666666">2*100/</span>STATS_sum)<span style="color: #666666">:</span>(<span style="color: #666666">1</span>)<span style="color: #666666">:</span><span style="color: #00A000">xticlabels</span>(<span style="#FF0000">$</span><span style="color: #666666">1*1E3</span>) lw <span style="color: #666666">2</span> <span style="color: #AA22FF">t</span><span style="color: #BB4444">""</span>
</pre></div>
</td></tr></table>
还有另一种简单点的作法, 使用下面的boxxyerrorbars方法.
数据及其分布
可采用两种方式
<table class="highlighttable"><th colspan="2" style="text-align:left">gnuplot</th><tr><td><div class="linenodiv" style="background-color: #f0f0f0; padding-right: 10px"><pre style="line-height:125%">1
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<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">x2tics</span> <span style="color: #666666">1</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">xtics</span> nomirror
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">xl</span><span style="color: #BB4444">"time(ps)"</span>; <span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">yl</span><span style="color: #BB4444">"RMSD(nm)"</span>; <span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">x2label</span> <span style="color: #BB4444">'</span>Freq<span style="color: #666666">%</span><span style="color: #BB4444">'</span>
<span style="#FF0000">stat</span> <span style="#FF0000">'fre</span><span style="color: #AA22FF; font-weight: bold">q</span><span style="#FF0000">.dat'</span> <span style="#FF0000">u</span> <span style="#FF0000">2</span> <span style="#FF0000">nooutput</span>
<span style="color: #AA22FF; font-weight: bold">plot</span> [][<span style="color: #666666">0:</span>] <span style="color: #BB4444">'</span>freq<span style="color: #666666">.</span>dat<span style="color: #BB4444">'</span> <span style="color: #AA22FF">u</span> (<span style="#FF0000">$</span><span style="color: #666666">2*100/</span>STATS_sum)<span style="color: #666666">:1:</span>(<span style="color: #666666">0</span>)<span style="color: #666666">:</span>(<span style="#FF0000">$</span><span style="color: #666666">2*100/</span>STATS_sum)<span style="color: #666666">:</span>(<span style="#FF0000">$</span><span style="color: #666666">1-.5*</span><span style="color: #AA22FF">w</span>)<span style="color: #666666">:</span>(<span style="#FF0000">$</span><span style="color: #666666">1+.5*</span><span style="color: #AA22FF">w</span>) <span style="color: #AA22FF">w</span> boxxyerrorbars <span style="color: #AA22FF">axes</span> x2y1 lc <span style="color: #666666">2</span> <span style="color: #AA22FF">t</span><span style="color: #BB4444">''</span><span style="color: #666666">,</span> \
<span style="color: #BB4444">'</span>C<span style="color: #666666">:</span><span style="#FF0000">\</span>Users<span style="#FF0000">\</span>Jicun<span style="#FF0000">\</span>Desktop<span style="#FF0000">\</span>_JOB<span style="#FF0000">\</span><span style="color: #666666">1</span>y57<span style="#FF0000">\</span>rmsd<span style="color: #666666">.</span>xvg<span style="color: #BB4444">'</span> <span style="color: #AA22FF">using</span> <span style="color: #666666">1:2</span> <span style="color: #AA22FF">w</span> l lw <span style="color: #666666">4</span> lc <span style="color: #666666">1</span> <span style="color: #AA22FF">t</span><span style="color: #BB4444">''</span>
</pre></div>
</td></tr></table>
<table class="highlighttable"><th colspan="2" style="text-align:left">gnuplot</th><tr><td><div class="linenodiv" style="background-color: #f0f0f0; padding-right: 10px"><pre style="line-height:125%"> 1
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<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">multi</span> lay <span style="color: #666666">1,1</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">rmargin</span> at screen <span style="color: #666666">0.8</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">xl</span><span style="color: #BB4444">"time(ps)"</span>; <span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">yl</span><span style="color: #BB4444">"RMSD(nm)"</span>
<span style="color: #AA22FF; font-weight: bold">plot</span> [<span style="color: #666666">0:</span>][<span style="color: #666666">0:</span>] <span style="color: #BB4444">'</span>C<span style="color: #666666">:</span><span style="#FF0000">\</span>Users<span style="#FF0000">\</span>Jicun<span style="#FF0000">\</span>Desktop<span style="#FF0000">\</span>_JOB<span style="#FF0000">\</span><span style="color: #666666">1</span>y57<span style="#FF0000">\</span>rmsd<span style="color: #666666">.</span>xvg<span style="color: #BB4444">'</span> <span style="color: #AA22FF">using</span> <span style="color: #666666">1:2</span> <span style="color: #AA22FF">w</span> l lw <span style="color: #666666">4</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">lmargin</span> at screen <span style="color: #666666">0.8</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">rmargin</span> at screen <span style="color: #666666">.99</span>
<span style="color: #AA22FF; font-weight: bold">unset</span> <span style="color: #AA22FF">xtics</span>; <span style="color: #AA22FF; font-weight: bold">unset</span> <span style="color: #AA22FF">ytics</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">mxtics</span> <span style="color: #666666">1</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">xtics</span> format <span style="color: #BB4444">" "</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">ytics</span> format <span style="color: #BB4444">" "</span>
<span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">xl</span><span style="color: #BB4444">" "</span>; <span style="color: #AA22FF; font-weight: bold">set</span> <span style="color: #AA22FF">yl</span><span style="color: #BB4444">" "</span>
<span style="#FF0000">stat</span> <span style="#FF0000">'fre</span><span style="color: #AA22FF; font-weight: bold">q</span><span style="#FF0000">.dat'</span> <span style="#FF0000">u</span> <span style="#FF0000">2</span> <span style="#FF0000">nooutput</span>
<span style="color: #AA22FF; font-weight: bold">plot</span> [][<span style="color: #666666">0:</span>] <span style="color: #BB4444">'</span>freq<span style="color: #666666">.</span>dat<span style="color: #BB4444">'</span> <span style="color: #AA22FF">u</span> (<span style="#FF0000">$</span><span style="color: #666666">2*100/</span>STATS_sum)<span style="color: #666666">:1:</span>(<span style="color: #666666">0</span>)<span style="color: #666666">:</span>(<span style="#FF0000">$</span><span style="color: #666666">2*100/</span>STATS_sum)<span style="color: #666666">:</span>(<span style="#FF0000">$</span><span style="color: #666666">1-.5*</span><span style="color: #AA22FF">w</span>)<span style="color: #666666">:</span>(<span style="#FF0000">$</span><span style="color: #666666">1+.5*</span><span style="color: #AA22FF">w</span>) <span style="color: #AA22FF">w</span> boxxyerrorbars <span style="color: #AA22FF">t</span><span style="color: #BB4444">''</span>
</pre></div>
</td></tr></table>
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