I have been using LAMMPS doing simulations for some systems consisting of rigid bodies. I recently found that using the "fix rigid" commands with a barostat (i.e., fix rigid/nve or rigid/nve/small combined with a Berdenson barostat, or fix rigid/npt, rigid/nph (with or without "/small")), the rigid bodies will slightly distorted about 0.1% of their length scale. For instant, if I run a simulation for a system consisting of 2-nm-sized rigid dimers in a NPT ensemble (300K, 1atm). The distance between the two beads in a dimer will slightly change between 19.99 to 20.01 Angstrom. I found this happened regardless the shape of the rigid bodies (dimers, polyhedrons, small molecules). The deform of the rigid body does not happen if no barostat is used (e.g., NVE, NVT ensembles)
The distortion is tiny, however, this precision does not meet the requirement for my current study. Therefore, I post this to seek helps. Any comments, suggestions, or answers are welcome. I suspect that the slight shape change of the rigid body is caused by the remapping procedure when applying a barostat (either Berdenson or Nose-Hoover). Does anyone know if this is true? More specifically, is it due to the (low) precision of the FFT used in the remap? If so, is there any way to increase the accuracy? Many thanks for your helps!!!
Department of Chemistry,
University of Utah