version 2May11, running in parallel on 48 cores
I am using ‘compute com/molecule’ to follow the center of mass of a molecule diffusing through a polymer matrix. I have been encountering a problem with the c.o.m. values produced by the com/molecule compute. The c.o.m. appears to be subject to an artifactual drift, such that the diffusive motion is biased in a certain direction.
I have attached an image, ‘com_drift.png’ of the c.o.m. trajectory in the xy (black); xz (red); and yz (green) planes, in which the drift behavior is evident. *(see more info at end of email). I have also attached the input files required to produce such artifactual c.o.m. behavior (datafile and infile).
I have found this directed drift in c.o.m. values in most simulations I have run, although it sometimes does not show up until a few hundred thousand steps. It always shows up if the simulation is run long enough. I am aware of the repeated warnings in the manual about how one must be careful with image flags. I have tried resetting image flags between different fixes (langevin, npt, nvt, etc.) in the simulation, which doesn’t seem to help things. Further, I notice that the drift occurs in many cases where the com of the diffusant molecule does not cross a periodic boundary. Finally, the c.o.m. values don’t jump in value, but rather experience a continuous drift, which seems to suggest that the problem is not related to crossing a periodic boundary.
Finally, you’ll notice that I have a brief langevin equilibration stage preceding the production npt stage. While switching fixes does seem to encourage the artifactual com trajectories, it is not required. I had relented and simply run a very long fix nvt sim and the drift behavior kicked in after a couple of million steps. The point is that you can play around with different fixes and resetting image flags, but this behavior will always appear at some point. Does anyone have any idea what might be causing this artifact?
Chris
*FYI, this c.o.m. trajectory in the xy/xz/yz planes can be obtained by running the following shell command on the c.o.m. trajectory data file, ‘com.dat’, output by lammps as part of the fix print command issued in the infile:
cat com.dat | grep -v [a-z] | awk ‘{print $2 " " $3}’ >> comtraj.dat ; echo >> comtraj.dat; cat com.dat | grep -v [a-z] | awk ‘{print $2 " " $4}’ >> comtraj.dat; echo >> comtraj.dat; cat com.dat | grep -v [a-z] | awk ‘{print $3 " " $4}’ >> comtraj.dat; xmgrace -nxy comtraj.dat
datafile.tar.gz (93.4 KB)
infile (1.15 KB)