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<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 am trying to simulate coarse-grained dodecane using MARTINI force field. One of the properties I would like to measure is viscosity. I was trying to do this from NEMD (actually I am using Langevin stochastic
dynamics) and I am facing the problem having negative(!) value for 1/eta calculated by g_energy.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">Am I missing something very obvious?<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 using 4.5.4 version.<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">Thank you very much in advance.<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">My .mpd file looks like:<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">integrator = sd<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">dt = 0.005<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">nsteps = 1000000<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">comm_mode = Linear<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">nstcomm = 100<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">nstxout = 10000 ; write coords<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">nstvout = 10000 ; write velocities<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">nstfout = 0 ; write forces (Do not write them)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">nstxtcout = 0 ; write coords to xtc-trajectory file<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">nstlog = 2000 ; print to logfile<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">nstenergy = 100 ; print energies<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">xtc_precision = 1000<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">xtc-grps =<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">energygrps = DEC<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">coulombtype = Shift<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">rcoulomb_switch = 0.0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">rcoulomb = 1.2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">epsilon_r = 15<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">vdw_type = Shift<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">rvdw_switch = 0.9<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">rvdw = 1.2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">DispCorr = No<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">tc-grps = DEC<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">tau_t = 2.0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">ref_t = 300<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">cos_acceleration = 0.1<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">Pcoupl = no<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">gen_vel = no<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">gen_temp = 300<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">gen_seed = 473529<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"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-family:"Arial","sans-serif";font-weight:normal">=============================================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-family:"Arial","sans-serif";font-weight:normal">Dr Mikhail Stukan<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">Schlumberger Dhahran Carbonate Research Center,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">Dhahran Techno Valley - KFUPM,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">P.O. Box 39011, Dammam / Doha Camp 31942,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";font-weight:normal">Kingdom of Saudi Arabia</span><span style="font-family:"Arial","sans-serif";font-weight:normal"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-family:"Arial","sans-serif";font-weight:normal">Tel: +966 3 331 6182<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-family:"Arial","sans-serif";font-weight:normal">Fax:+966 3 330 0845<br>
<a href="mailto:mstukan@slb.com"><span style="color:blue">mstukan@slb.com</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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