Hello Lammps community,

First of all, I would like to apologize if my question is not directly related to Lammps.

I have a possibly simple question about the sampling quality, not the Lammps itself. To equilibrate my system (A bead-on-spring linear polymer of length 2000 monomers crowded by WCA beads in a cylindrical condiment), I use Langevin thermostat and fix NVE/limit with dt=0.01 and 10e6 timesteps.

I then run the system with dt=0.005 for 5e7 timesteps in the sampling phase. I dump the configurations of the system every 1000 timesteps in the sampling phase.

I use the block-averaging to estimate the statistical uncertainty in my system, as described the standard textbooks on computer simulations (Allen and Tildeskey, Rapaport, Frenkel & Smith). If I use the dumped configuration to estimate the statistical uncertainty, I have 5e4 configurations instead of the original 5e7 ones. Because of this reduced number of configurations, the number of block operations that can be done on 5e4 configurations is significantly smaller than the number of block operations can be done on the original 5e7 configurations. Does this cause any problems in reaching the plateau that should be seen in block-averaging method?

Let’s give an example, I use the dumped 5e4 configuration to compute the radius of gyration of the polymer and then use the block-averring method to find the statistical uncertainty in the mean radius of gyration of the polymer. According to the attached plot, the system is not run enough to reach equilibrium since there is no plateau in the statistical uncertainty vs the number of block operations. Has this failure in reaching the equilibrium happened due to the reduced number of configurations (5e4 instead of 5e7)? Or, even if I used the total number of configurations, I would not still see the plateau? If I used the all the configuration, I had 25 block operations instead of 14 operations - the vertical line for each data point shows the standard error for that data point.

According to the textbooks and the original paper (https://aip.scitation.org/doi/abs/10.1063/1.457480?casa_token=9nGutL6jMI8AAAAA:zr2RSixcQCFqa4_40IUvBZsOB_kAoprc8gvgi9VJPPlgUQXcmVXzFMgUPgyUtrINyusmkw5G3Oo) on the block-averaging technique, one can see the plateau after 6-8 block-operation.

This experience triggered a more fundamental question for me: How can I check whether the system has reached equilibrium or not? Can I do this check on-the-fly in lammps?

Since my question is not about a lammps problem, I do not include a log file.

Thank you in advance for your answers.

Kind regards,

Amir

N80epsilon5.0r3.5lz13.5sig0.2nc41472dtbdump1000adump1000ens4_gyr_plot_err.pdf (16.5 KB)