Hello,
I am a new to classical MD and LAMMPS. I want to calculate some properties of my system in NVT ensemble at 300K. The strategy I am using is described as follows (in serial order):
(i) minimize: the structure to really small forces.
(ii) NVE: to equilibrate the minimized structure.
(iii) NVT: to 300K using Nose-Hoover thermostat.
(iv) NPT: since the volume was always fixed in the above calculations, I thought, I will perform NPT at 300K and 0 bar to get the correct volume, and atomic coordinates.
(v) NVE: to equilibrate the output system from NPT.
(vi) Finally, NVT at 300K to perform measurements I need.
Is the above wrong/too much ? What should be the correct strategy ?
In the above I face some problems. The output pressure is actually 0 at the end of the step (ii) and (iii). But the pressure fluctuates to several tens of thousand bars in NPT stage (step iv). As a result I get wrong atomic coordinates and structure. I read the forum and found that Nose Hoover barostat can fluctuate a lot. So, I have been playing with drag parameter in Nose Hoover. Upto certain steps, quantities are fine, but a sharp change in volume and pressure happens at some step in step (iv), ie. NPT. Then pressure starts fluctuating quite a bit and never stabilizes and the structure also goes bad.
Finally, I decided to change from NPT to:
fix 1 all nvt temp 300.0 300.0 100.0
fix 2 all press/berendsen iso 0.0 0.0 100000.0
I figured, the simulation is very sensitive to Pdamp above. When Pdamp = 1000, several quantities such as volume, pressure, etc. become “nan” very quickly, so, changed Pdamp = 10000. It ran well for some time and then the program stopped. Currently, I am running with Pdamp = 100000. It is still running.
My question is:
(i) If my strategy described above in steps (i) to (vi) is ok ? Do I need to relax volume after NVE and NVT for calculation of actual quantities or since the pressure is zero after NVE and NVT, it is alright to go ahead with other calculations without any need to perform NPT ?
(ii) How to choose the parameters of NPT (or press/berendsen) correctly for a given a system ?
Thanks,
George