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<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">Dear gmx-users,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">I am currently trying to simulate a thermalized wall of coarse-grained particles. I model the wall in the framework of the bead on spring approach. The wall molecules are
defined as dimers :<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";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";font-weight:normal">[ moleculetype ]<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal">; molname nrexcl<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal"> ROCK 1<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";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";font-weight:normal">[ atoms ]<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";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-size:9.0pt;font-family:"Courier New";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-size:9.0pt;font-family:"Courier New";font-weight:normal"> 2 FRC 1 ROCK FRC 2 0
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";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";font-weight:normal">[bonds]<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal">; i j funct length force.c.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal"> 1 2 1 0.0 1000<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">And then the beads of one type (FRC) are defined to be fixed and no thermostat is applied to them. There are no interactions between the particles in the system (ensemble
of ideal harmonic oscillators):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal">energygrps = FRC PRC</span><span style="font-family:"Arial","sans-serif";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";font-weight:normal">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";font-weight:normal">tc-grps = PRC FRC<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal">tau_t = 0.5 0
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal">ref_t = 300 0
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal">freezegrps = FRC<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal">freezedim = Y Y Y<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal">energygrp_excl = FRC FRC FRC PRC PRC PRC<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Courier New";font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">The problem I have is that when I build the velocity distribution for the mobile particles (atom type PRC), the distribution does not correspond to the Maxwell’s distribution
(is shifted to the left). Am I missing something very basic? In my previous simulations for the same system but using another MD code with stochastic (DPD) thermostat the Maxwellian distribution was reproduced without any problem.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">Many thanks in advance,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">Mikhail<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
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