<div dir="ltr">I have been able to get the molecules to become more homogenous. The problem was I wasn't running the system long enough. I looked at the energy of the system though and am getting very large fluctuations. The system was ran with the initial temperature set at 300K by setting inital velocities, but the average temperature is very high and fluctuates alot. Here is what g_energy outputs for temperature, pressure, and total energy. Any ideas on how to keep the fluctuations down.<br>
<br>Statistics over 220001 steps [ 0.0000 thru 110.0000 ps ], 3 data sets<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>
Total Energy 4.20431e+15 6.35463e+14 6.15468e+14 4.98049e+12 5.47857e+14<br>Temperature 5.62218e+13 8.49769e+12 8.23031e+12 6.66013e+10 7.32618e+12<br>Pressure (bar) 6.10308e+12 9.22454e+11 8.93429e+11 7.2298e+09 7.95282e+11<br>
Heat Capacity Cv: 12.9143 J/mol K (factor = 0.022845)<br><br>; RUN CONTROL PARAMETERS<br>integrator = md <br>; Start time and timestep in ps<br>tinit = 0<br>dt = 0.0005<br>
nsteps = 2000000<br>; For exact run continuation or redoing part of a run <br>init_step = 0 <br>; mode for center of mass motion removal<br>comm-mode = Angular<br>
; number of steps for center of mass motion removal<br>nstcomm = 1 <br>; group(s) for center of mass motion removal<br>comm-grps = UNK <br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>
gen_vel = yes<br>gen_temp = 300<br>gen_seed = 1993<br><br>Thanks for any input,<br>Andy<br><br><br><br><div class="gmail_quote">On Tue, Aug 26, 2008 at 1:56 PM, Vitaly Chaban <span dir="ltr"><<a href="mailto:chaban@univer.kharkov.ua">chaban@univer.kharkov.ua</a>></span> wrote:<br>
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<p>Could you provide a movie or at least snapshots? What about energy of the system? How it changes?</p><div><div></div><div class="Wj3C7c">
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<p><span>Sorry I am not very good at describing my system. After running the simulation for a while or equilibrating the system all the oxygen molecules move along one wall (a rectangular box with the long side in the z direction and the shorter sides in the x and y direction at the origin) of my periodic boundary condition box. The nitrogen molecules stay fairly evenly distributed in the simulation box. I checked all the parameters and the charges were set to 0. I have about 175.2 g/l nitrogen and 56.5 g/l oxygen in my system. I realize this is higher pressure than atmosphere and have purposely done this.</span></p>
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<p><span>Andy</span></p>
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<p><span>On Tue, Aug 26, 2008 at 5:28 AM, Vitaly Chaban <</span><a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a><span>> wrote:</span></p>
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<p><span>> Using the parameters listed earlier I equalized my system after trying to</span></p>
<p><span>> place the oxygen and nitrogen molecules evenly throughout my system. The</span></p>
<p><span>> result showed the nitrogen molecules fairly even throughout the system but</span></p>
<p><span>> all the oxygen molecules on one side. Any ideas on why the system might not</span></p>
<p><span>> be equalizing out to an even distribution of oxygen by nitrogen?</span></p>
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<p><span>What's the density of O2 and N2 in your system?</span></p>
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<p><span>What's "all the oxygen molecules on one side"? What side?</span></p>
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<p><span>Are you sure no occasional charges are present on some site in your</span></p>
<p><span>system?</span></p>
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<p><span>--</span></p>
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<p><span>Vitaly V. Chaban</span></p>
<p><span>School of Chemistry</span></p>
<p><span>National University of Kharkiv</span></p>
<p><span>Svoboda sq.,4, Kharkiv 61077, Ukraine</span></p>
<p><span>email: </span><a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a></p>
<p><span>skype: vvchaban</span></p>
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</div></div><p><span>-- </span></p><div class="Ih2E3d">
<p><span>Vitaly V. Chaban</span></p>
<p><span>School of Chemistry</span></p>
<p><span>National University of Kharkiv</span></p>
<p><span>Svoboda sq.,4, Kharkiv 61077, Ukraine</span></p>
<p><span>email: </span><a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a></p>
<p><span>skype: vvchaban</span></p>
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