Dilraj Lama wrote:
Hello gmx users,
I have a query and would be greatfull if I could get some
suggestions on the subject.
I constructed a "tfe.itp" file with the
parameters mentioned by Fioroni et. al., J.
Phys. Chem. B 2000, 104, 12347-12354. I then
generated a "tfe.gro" file using InisghtII
molecular modeling package followed by
genconf.
I ran a "energy minimization" fand then a 2ns NPT ensemble Molecular
Dynamics simulation on the system.
Why are you not equilibrating before running a production simulation?
See http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
I did not specify "Lincs algorithm" in the parameter file to constrian the
bonds, rather I used [constraints] for bond distance in the "tfe.itp" file
itself.
I tried using tau_p as 1ps to 3 ps, but in doing so, my simulation crashed
after a certain period with the error message as "high pressure scaling,
and the failure of the constraint algorithm (either lincs or shake)".
See above.
So I used tau_p as 4 ps which is the value used for simulation in the
paper mentioned above.
The isothermal compressibility for liquid TFE at 298K is 1.22e-4
The density of TFE at 298K is 1383 Kg/m3.
These values are mentioned in the paper.
I then calculated the Properties "Temperature, pressure and density" for
the simulation using "g_energy".The average vaules for the properties are
as:
Temperature: 300.67
Density: 1402.95
Pressure: -2.59
Is the density value reasonable???
No, because of the above.
Why is the pressure value so different?????
For a 2ns simulation starting from generated velocities this is
surprisingly close to ref_p. See the above, and also
http://wiki.gromacs.org/index.php/Pressure_Coupling for a partial
discussion, and the GROMACS manual for a fuller one.
I would be very greatfull If I could get some suggestions on the
parameters and on the values of the properties mentioned.
It sounds like some doing some more background reading and doing some
tutorial material would be helpful to you.
Mark
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