Hello all, I have a system of tip3p water confined between two walls and the density profile still appears asymmetric at long times. The density profile is computed using fix ave/chunk command. The system has 13,000 water atoms and 1000 wall atoms. System is non-periodic in z. Walls are uncharged. System properties like KE and PE appear converged and stable at 300K and 1 atm. I initially assumed it may be an equilibration problem. But at 25ns, I am not so sure anymore. I’d appreciate your thoughts and suggestions.
Thank you both for your suggestions. The chunks definition is symmetric wrt the location of the walls actually. Also, increasing PPPM didn’t seem to change the result.
However, the problem was rectified when I removed the fix recenter command. I had assumed the fix recenter shouldn’t affect dynamics from the documentation. Although, I am not sure exactly how and why, but I suspect that having fix spring for the wall and fix recenter for all the atoms in the system caused the asymmetry. Anyway, removing fix recenter solves the problem.
Hi @mjksho,
It’s hard to figure out the origin of you issue without the input file but your walls might be slightly asymmetric with regard to your recenter coordinate. The INIT you use might not be exactly at the center of the box when the command is invoked.
Also you might want to zero out the total initial velocity with a velocity all zero linear command and zero out both Langevin random forces with the zero yes keyword. This might help you avoid future issues in your simulation. I think the tethered atoms eventually absorb the momentum but I don’t know much about your model.
@Germain, thanks for your comment. I actually attached the input file in the original post. Hmmn, I actually didn’t think to check that the INIT should be exactly at the center of the box. I will do a check of that and see if it solves the problem. Thanks for the tip on zeroing the momentum. I actually do this when I use the Langevin thermostat, but this was an oversight. Thanks for this.
