<div dir="ltr">The system works now, thanks for finding a simple mistake. Another question I had is if I want to calculate the average velocities of all the atoms over a period of time can I use g_traj to create an average velocity of the atoms, but looking at all_veloc.xvg file the atom number starts at 0 so I don't know where to cross reference it with another file to coordinates of that atom. Is there a function in GROMACS that will give averages of velocities and positions of atoms?<br>
<br>Thanks,<br>Andy<br><br><div class="gmail_quote">On Tue, Sep 2, 2008 at 3:25 PM, Vitaly Chaban <span dir="ltr"><<a href="mailto:chaban@univer.kharkov.ua">chaban@univer.kharkov.ua</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
<p> 1NIT N1 1 -0.552 0.004 -0.026</p>
<p> 1NIT N2 2 0.552 -0.004 0.026</p>
<p> 2.00000 2.00000 1.20000</p>
<p><br></p>
<p>Andy,</p>
<p><br></p>
<p>If I were your system, I would explode immediately and never let run myself again.</p>
<p><br></p>
<p><br></p>
<p>b0 (N-N) = (0.552+0.552)=1.104 nm. How should the system behave with such unrealistic solvent and huge energies respectively?</p>
<p><br></p>
<p><br></p>
<p>AS> Vitaly,</p>
<p>AS> </p>
<p>AS> Attached is all the files for my forcefield. In ffgmxnb.itp there are two sets of data used for C-N, C-O, and O-N. One set of data is from literature I found and is commented out. The other is from combining like in the gromacs manual with the values given from the ffgmxnb.itp file. Thanks for the help.</p>
<p>AS> </p>
<p>AS> Andy</p>
<p>AS> </p>
<p>AS> </p>
<p>AS> On Tue, Sep 2, 2008 at 10:00 AM, Vitaly Chaban <<a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a>> wrote:</p>
<p>AS> </p>
<p>AS> You have problems with your force field.</p>
<p>AS> </p>
<p>AS> If you send me all the files describing your system I'll try to see</p>
<p>AS> what really happens when I have free time..</p>
<p>AS> </p>
<p>AS> </p>
<p>AS> 2008/9/2 Andy Shelley <<a href="mailto:robert.shelley@gmail.com" target="_blank">robert.shelley@gmail.com</a>>:</p>
<p>AS> </p><div><div></div><div class="Wj3C7c">
<p>>> I have been able to get the molecules to become more homogenous. The problem</p>
<p>>> was I wasn't running the system long enough. I looked at the energy of the</p>
<p>>> system though and am getting very large fluctuations. The system was ran</p>
<p>>> with the initial temperature set at 300K by setting inital velocities, but</p>
<p>>> the average temperature is very high and fluctuates alot. Here is what</p>
<p>>> g_energy outputs for temperature, pressure, and total energy. Any ideas on</p>
<p>>> how to keep the fluctuations down.</p>
<p>>></p>
<p>>> Statistics over 220001 steps [ 0.0000 thru 110.0000 ps ], 3 data sets</p>
<p>>></p>
<p>>> Energy Average RMSD Fluct. Drift</p>
<p>>> Tot-Drift</p>
<p>>> -------------------------------------------------------------------------------</p>
<p>>> Total Energy 4.20431e+15 6.35463e+14 6.15468e+14 4.98049e+12</p>
<p>>> 5.47857e+14</p>
<p>>> Temperature 5.62218e+13 8.49769e+12 8.23031e+12 6.66013e+10</p>
<p>>> 7.32618e+12</p>
<p>>> Pressure (bar) 6.10308e+12 9.22454e+11 8.93429e+11 7.2298e+09</p>
<p>>> 7.95282e+11</p>
<p>>> Heat Capacity Cv: 12.9143 J/mol K (factor = 0.022845)</p>
<p>>></p>
<p>>> ; RUN CONTROL PARAMETERS</p>
<p>>> integrator = md</p>
<p>>> ; Start time and timestep in ps</p>
<p>>> tinit = 0</p>
<p>>> dt = 0.0005</p>
<p>>> nsteps = 2000000</p>
<p>>> ; For exact run continuation or redoing part of a run</p>
<p>>> init_step = 0</p>
<p>>> ; mode for center of mass motion removal</p>
<p>>> comm-mode = Angular</p>
<p>>> ; number of steps for center of mass motion removal</p>
<p>>> nstcomm = 1</p>
<p>>> ; group(s) for center of mass motion removal</p>
<p>>> comm-grps = UNK</p>
<p>>></p>
<p>>> ; GENERATE VELOCITIES FOR STARTUP RUN</p>
<p>>> gen_vel = yes</p>
<p>>> gen_temp = 300</p>
<p>>> gen_seed = 1993</p>
<p>>></p>
<p>>> Thanks for any input,</p>
<p>>> Andy</p>
<p>>></p>
<p>>></p>
<p>>></p>
<p>>> On Tue, Aug 26, 2008 at 1:56 PM, Vitaly Chaban <<a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a>></p>
<p>>> wrote:</p>
<p>>>></p>
<p>>>> Could you provide a movie or at least snapshots? What about energy of the</p>
<p>>>> system? How it changes?</p>
<p>>>></p>
<p>>>></p>
<p>>>> ></p>
<p>>>></p>
<p>>>> Sorry I am not very good at describing my system. After running the</p>
<p>>>> simulation for a while or equilibrating the system all the oxygen molecules</p>
<p>>>> move along one wall (a rectangular box with the long side in the z direction</p>
<p>>>> and the shorter sides in the x and y direction at the origin) of my periodic</p>
<p>>>> boundary condition box. The nitrogen molecules stay fairly evenly</p>
<p>>>> distributed in the simulation box. I checked all the parameters and the</p>
<p>>>> charges were set to 0. I have about 175.2 g/l nitrogen and 56.5 g/l oxygen</p>
<p>>>> in my system. I realize this is higher pressure than atmosphere and have</p>
<p>>>> purposely done this.</p>
<p>>>></p>
<p>>>> Andy</p>
<p>>>></p>
<p>>>> On Tue, Aug 26, 2008 at 5:28 AM, Vitaly Chaban <<a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a>></p>
<p>>>> wrote:</p>
<p>>>></p>
<p>>>> > Using the parameters listed earlier I equalized my system after trying</p>
<p>>>> > to</p>
<p>>>></p>
<p>>>> > place the oxygen and nitrogen molecules evenly throughout my system.</p>
<p>>>> > The</p>
<p>>>></p>
<p>>>> > result showed the nitrogen molecules fairly even throughout the system</p>
<p>>>> > but</p>
<p>>>></p>
<p>>>> > all the oxygen molecules on one side. Any ideas on why the system might</p>
<p>>>> > not</p>
<p>>>></p>
<p>>>> > be equalizing out to an even distribution of oxygen by nitrogen?</p>
<p>>>></p>
<p>>>> What's the density of O2 and N2 in your system?</p>
<p>>>></p>
<p>>>> What's "all the oxygen molecules on one side"? What side?</p>
<p>>>></p>
<p>>>> Are you sure no occasional charges are present on some site in your</p>
<p>>>></p>
<p>>>> system?</p>
<p><br></p>
<p><br></p>
<p><br></p>
</div></div></div>
</blockquote></div><br></div>