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<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">Dear gmx-users,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">I have performed further investigation on the subject of the velocity distribution
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><a href="http://lists.gromacs.org/pipermail/gmx-users/2011-April/060316.html">http://lists.gromacs.org/pipermail/gmx-users/2011-April/060316.html</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">and what I found looks like a sort of a bug to me. Namely, the velocity distribution profiles are different if I simulate a thermalized wall via dimmers with one on the particles being fixed:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">====================================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal">[ moleculetype ]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal">; molname nrexcl<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal"> ROCK 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal">[ atoms ]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal">;id type resnr residu atom cgnr charge<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal">1 PRC 1 ROCK PRC 1 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal">2 FRC 1 ROCK FRC 2 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal">[bonds]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal">; i j funct length force.c.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;font-weight:normal"> 1 2 1 0.0 1000<o:p></o:p></span></p>
<pre><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">====================================<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">energygrps = FRC PRC<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">tcoupl = v-rescale<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">tc-grps = PRC FRC<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">tau_t = 0.5 0<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">ref_t = 300 0<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">freezegrps = FRC<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">freezedim = Y Y Y<o:p></o:p></span></pre>
<pre><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">energygrp_excl = FRC FRC FRC PRC PRC PRC<o:p></o:p></span></pre>
<p class="MsoNormal"><span style="font-weight:normal">===================================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">or using position_restraints approach:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">====================================<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal">[ moleculetype ]<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal">; molname nrexcl<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal"> ROCK 1<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal">[ atoms ]<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal">;id type resnr residu atom cgnr charge<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal">1 PRC 1 ROCK PRC 1 0
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal">[ position_restraints ]<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal">; iatom type fx fy fz<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal">1 1 10000 10000 10000<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal">==================================<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">energygrps = PRC</span><span style="font-weight:normal"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">tcoupl = v-rescale
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">tc-grps = PRC
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">tau_t = 0.5
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">ref_t = 300
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New"">energygrp_excl = PRC PRC<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">==============================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">For both simulations I built the velocity distribution function using g_traj.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">In both cases the average kinetic temperature (I have calculated it from the averaged kinetic energy based on the velocity distributions) corresponds well to the one assigned to the thermostat (300 K).
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">But, a) the velocity distributions for these two cases differ from each other; b) neither of them is Maxwellian.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">In my simulations I use 4.5.3 version of GROMACS.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">I am really lost and would very much appreciate any comments.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">Many thanks in advance.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">Mikhail. <o:p></o:p></span></p>
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