Pressure of system

LAMMPS LAMMPS Beginners
1

Dears
hope you are doing well
I want to calculate the pressure of the system in both repulsive and attractive interaction and I want to be around (3000 atm) and (- 1000 atm) but I got at 0 time step around 330000 atm and after some time step I got pressure in minuses ranging from (122 to 1600) as in attached file. My question are how I can the pressure of system, Is the pressure at 0 timestep included the calculations , how I can decease it, and what is large negative pressure and large positive pressure is that determined from output log file?
in.input.test.3.lmp (1.7 KB)
log.lammps (9.9 KB)

2

Without the data and molecule files, it’s tough to say for certain, but looking at your bond lengths and number of atoms in the molecule, I’m guessing that you have some slightly overlapping atoms when you create them randomly. This causes the high pressure and energy at the start. They move away without crashing the simulation, reducing it. The fluctuations around your “expected” value seem typical for ~100k atoms.

The biggest issue is that warning: you shouldn’t use both fix nve and fix nvt at the same time.

3

Your input is full of bad ideas, inconsistencies, and errors. It is no surprise that you get undesired behavior.

You need more help than you can get from an online forum. You also need a proper understanding of the models and methods.

4

Dear akohlmey
I appreciate your replying to my questions. I really appreciate if you mention some points or error it will be very helpful to me so I can take some experience

Regards

5

Dear Michael_jacobs

Many thanks for you help, I attached molecule data file. Also please how can I solve problem of overlapping atoms problem?

Regards
PDMS.mol (2.2 KB)

6

I don’t have the time to go over all the details. Some issues require lengthy explanations because your inputs and questions clearly show that you are lacking significant fundamental understanding and training of both the models and the MD methodology and good practices. At that point it is almost useless to even list the errors since your next question will obviously be what you need to do and it is not my job and I don’t have the time or interest to do your work for you.

Just a quick list:

  • your force field is not suitable, or you are using the wrong pair style and atom style and not setting properties required by the force field
  • your system creation is bad
  • your time integration is bogus
  • you are ignoring warnings that you should not ignore
  • for your kind of system it is very bad to ignore lost atoms
  • there is no equilibration protocol