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?
Thanks, Andy On Tue, Sep 2, 2008 at 3:25 PM, Vitaly Chaban <[EMAIL PROTECTED]>wrote: > 1NIT N1 1 -0.552 0.004 -0.026 > > 1NIT N2 2 0.552 -0.004 0.026 > > 2.00000 2.00000 1.20000 > > > Andy, > > > If I were your system, I would explode immediately and never let run myself > again. > > > > b0 (N-N) = (0.552+0.552)=1.104 nm. How should the system behave with such > unrealistic solvent and huge energies respectively? > > > > AS> Vitaly, > > AS> > > 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. > > AS> > > AS> Andy > > AS> > > AS> > > AS> On Tue, Sep 2, 2008 at 10:00 AM, Vitaly Chaban < > [EMAIL PROTECTED]> wrote: > > AS> > > AS> You have problems with your force field. > > AS> > > AS> If you send me all the files describing your system I'll try to see > > AS> what really happens when I have free time.. > > AS> > > AS> > > AS> 2008/9/2 Andy Shelley <[EMAIL PROTECTED]>: > > AS> > > >> 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? > > > > >
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