Hello,
I am using the LAMMPS (3 Mar 2020). I have generated the initial positions of a polymer CG model for a volume so that the target mass density is achieved. In order to equilibrate the system (to get the desired segregated microstructure), I run an NVT (with minimize) simulation at a higher temperature, then bring it down to room temperature in the second step (NVT with minimize) and finally equilibrate at room temperature (NVT with minimize). Kindly correct me if I am doing it wrong.
Secondly, in the above procedure, I am getting an error of missing atoms in the first step itself. After going through suggestions to overcome the issue, I increased the initial volume eight times. Now the simulation proceeds, but there is a sudden increase in temperature, which reduces over time. Also, the normal pressures are of order 10^3 MPa (desired 0.1 MPa) , which reduces slowly over time. I do not understand that even though the density is eight times lower than the actual one, how come the normal pressures be so high. The question is whether I am following the correct approach towards equilibration, if not kindly suggest the alternative.
I have also attached the input header file herewith. I look forward to hearing from you soon. Thank you very much for your time and help.
With best wishes,
Arunjyoti Sinha Roy.
Input_Header_microstructure_equilibration.in (2.77 KB)
You should be aware that setting up the initial structure is vital in polymer systems, due to the very long time scales required to reach equilibrium conditions if you start far from it. This is true for liquid-phase polymer systems, and even more so for solid ones. It is impossible to give specific advice without knowing the details of your system.
Note also that a bad initial structure for polymers can exhibit frustration: large strain localized on certain angles or dihedrals, which cannot be relaxed without a major reorganization of the system. There may be voids in the system (thus a low density) but it’s the bonded forces that dominate the stress in that case. If the chains are long enough to be subject to entanglement, a bad structure cannot be equilibrated just by simulation.
Try investing some time investigating better ways to prepare the initial structure from the literature, which will be even more important than sampling time.
Giacomo
the symptoms you describe would be most easily explained with having a bad bond topology, i.e. atoms that are connected to the “wrong” periodic copy and other similar issues.
your molecules would be somewhat twisted and contorted and are trying to restructure themselves, but cannot because of the non-bonded interactions “jamming” every attempt to significantly reorient. that this is less of a problem, if you expand the system would be consistent with that.
the best way to deal with this would be to review the process of building the initial structure. when using a visualization tool to inspect the structure, you need to make certain that it reads the bond topology from the data file and not guesses it from distances (which many programs will do when reading files without that information). that will give you the wrong impression.
another option to try is to change the non-bonded pair style to “soft” and start by making it very “soft” at the beginning. then the system can better unoverlap and resolve contortions. after the system has relaxed the bond topology, you can ramp up the soft potential, e.g. with fix adapt and slowly approach the point where atoms repel each other like they should. then you can switch to your intended force field and continue the equilibration.
ultimately, to be certain, you should talk to somebody local with experience. the mailing list is a not a good place to get advice that is specific to your research. it is almost always better to talk to people that understand that research (and care about it).
axel.