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

[Vitaly Chaban]

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 <robert.shelley at gmail.com>:
> 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
>



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