[gmx-users] Re: Re[4]: Using Morse potentials with ENCAD force field

Fri Sep 5 18:59:17 CEST 2008

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 <chaban at univer.kharkov.ua>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 <
> chaban at univer.kharkov.ua> 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 <robert.shelley at gmail.com>:
>
> 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 <
> chaban at univer.kharkov.ua>
>
> >> 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 <
> chaban at univer.kharkov.ua>
>
> >>> 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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