Thanks so much for your patience and nice reply. I really appreciate those unsung heroes, just like you, aidan…
I carefully thought about your comments and want to find some possible solutions to calculate what I want to do using LAMMPS.
a) npt and nvt are the wrong ensembles for this kind of system,
at least for production. you want nve and non-periodic boundaries.
b) the “macroscopic” pressure for your system needs to be
computed differently than for a bulk system.
c) of course the volume of your system is the volume of the
simulation cell not just the enclosed volume of your setup.
In order to aviod the above mentioned problems. Perhaps I could use something like a piston to add a force/pressure on fluid with the system controlling by langevin thermostat. Here, the force direction should be non-periodic.
I did several tests and fond that in NPT('fix 2 part2 npt temp 300.0 300.0 10.0 z 1000.00 1000.00 10.0 dilate partial '), the temperature of fluid (part2) was always fluctuate around 350K but not the needed one (300K). Beside, the temperature of the entire system keeping 300K. That is to say, 50 K should be substracted from the fluid atoms. I changed the input fix command like this:
'fix 2 part2 npt temp 250.0 250.0 10.0 z 1000.00 1000.00 10.0 dilate partial.
Then, fluid temperature fluctuated around 300K. After NPT, another NVT was performed:
'fix 3 part2 nvt temp 300.0 300.0 10.0 ’
Fluid temperature was also 300K.
Now, it seems everything looks good. Just like what you said, something like very rare “two wrongs make a right” kind of deals ’ happened. I believe it is caused by some wrong volume issue and I think I need to add a piston than perform NPT in the system.
Thanks very much,