You have problems with your force field. If you send me all the files describing your system I'll try to see what really happens when I have free time..
2008/9/2 Andy Shelley <[EMAIL PROTECTED]>: > 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. > > Statistics over 220001 steps [ 0.0000 thru 110.0000 ps ], 3 data sets > > Energy Average RMSD Fluct. Drift > Tot-Drift > ------------------------------------------------------------------------------- > Total Energy 4.20431e+15 6.35463e+14 6.15468e+14 4.98049e+12 > 5.47857e+14 > Temperature 5.62218e+13 8.49769e+12 8.23031e+12 6.66013e+10 > 7.32618e+12 > Pressure (bar) 6.10308e+12 9.22454e+11 8.93429e+11 7.2298e+09 > 7.95282e+11 > Heat Capacity Cv: 12.9143 J/mol K (factor = 0.022845) > > ; RUN CONTROL PARAMETERS > integrator = md > ; Start time and timestep in ps > tinit = 0 > dt = 0.0005 > nsteps = 2000000 > ; For exact run continuation or redoing part of a run > init_step = 0 > ; mode for center of mass motion removal > comm-mode = Angular > ; number of steps for center of mass motion removal > nstcomm = 1 > ; group(s) for center of mass motion removal > comm-grps = UNK > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = yes > gen_temp = 300 > gen_seed = 1993 > > Thanks for any input, > Andy > > > > On Tue, Aug 26, 2008 at 1:56 PM, Vitaly Chaban <[EMAIL PROTECTED]> > wrote: >> >> Could you provide a movie or at least snapshots? What about energy of the >> system? How it changes? >> >> >> > >> >> 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. >> >> Andy >> >> On Tue, Aug 26, 2008 at 5:28 AM, Vitaly Chaban <[EMAIL PROTECTED]> >> wrote: >> >> > Using the parameters listed earlier I equalized my system after trying >> > to >> >> > place the oxygen and nitrogen molecules evenly throughout my system. >> > The >> >> > result showed the nitrogen molecules fairly even throughout the system >> > but >> >> > all the oxygen molecules on one side. Any ideas on why the system might >> > not >> >> > be equalizing out to an even distribution of oxygen by nitrogen? >> >> What's the density of O2 and N2 in your system? >> >> What's "all the oxygen molecules on one side"? What side? >> >> Are you sure no occasional charges are present on some site in your >> >> system? >> >> -- >> >> Vitaly V. Chaban >> >> School of Chemistry >> >> National University of Kharkiv >> >> Svoboda sq.,4, Kharkiv 61077, Ukraine >> >> email: [EMAIL PROTECTED] >> >> skype: vvchaban >> >> >> >> >> -- >> >> Vitaly V. Chaban >> >> School of Chemistry >> >> National University of Kharkiv >> >> Svoboda sq.,4, Kharkiv 61077, Ukraine >> >> email: [EMAIL PROTECTED] >> >> skype: vvchaban > -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
