Hello LAMMPS users,
I am running a simple simulation in an attempt to isolate a problem with using rigid bodies. I have 3 to 5 H2O molecules in a cube with periodic boundary conditions. The H2O molecules consist of 3 beads and have a ‘fix rigid’ applied so that hydrogens will not separate from the oxygens. Pair potentials between the molecules are governed by lj/cut between the oxygens. I use a langevin thermostat to maintain a constant temperature. The log file is set to track the temperature and kinetic energy. Units are in nondimensional lj.
The issues arise from the log file where the kinetic energy (not the temperature) appears to fluctuate around the value of my desired temperature. In addition, the degrees of freedom is unexpected. According to ‘compute temp’ documentation, temperature is supposed to be calculated by summation of (1/2)mv^2 = (d/2)NkT. For my 3D system, this means the average kinetic energy should be (3/2)kT. Using the results from my log file, I find the degrees of freedom or the ratio of average kinetic energy to temperature varies by number of molecules: 5/6 for 3 molecules and 9/10 for 5 molecules. Is there an explanation that I am overlooking in regards to the kinetic energy and temperature when I use ‘fix rigid’? I can provide my data and log files if you feel those would help.
Thanks in advance,