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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