[gmx-users] Re: Re[2]: Using Morse potentials with ENCAD force field

[Andy Shelley]

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?
>
>
>
> --
>
>
> Vitaly V. Chaban
>
> School of Chemistry
>
> National University of Kharkiv
>
> Svoboda sq.,4, Kharkiv 61077, Ukraine
>
> email: chaban at univer.kharkov.ua
>
> skype: vvchaban
>
>
>
>
>
>
> --
>
> Vitaly V. Chaban
>
> School of Chemistry
>
> National University of Kharkiv
>
> Svoboda sq.,4, Kharkiv 61077, Ukraine
>
> email: chaban at univer.kharkov.ua
>
> skype: vvchaban
>
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