Dear all
I run a standard MD simulation using the NVT integrator, applying usual CHARMM force fields. My system consists of an amino acid dissolved in TIP3P water confined between a carbon slit pore represented by 9/3 LJ walls. The total energy of the system is kept constant (apart from usual fluctuations) by the NVT integrator up to 40 million time steps, then something strange happens: the energy suddenly starts to go down, in the same time the temperature fluctuations are remarkably reduced. I started the simulation now for the second time and the behavior is always the same. Has anybody an idea what happens there? I attached plots of the total temperature and energy.
Thank you for your help
Sabine
energy.pdf (29.4 KB)
temp.pdf (61.4 KB)
Dear all
dear sabine,
I run a standard MD simulation using the NVT integrator, applying usual
CHARMM force fields. My system consists of an amino acid dissolved in
TIP3P water confined between a carbon slit pore represented by 9/3 LJ
walls. The total energy of the system is kept constant (apart from
usual fluctuations) by the NVT integrator up to 40 million time steps,
then something strange happens: the energy suddenly starts to go down,
in the same time the temperature fluctuations are remarkably reduced.
I started the simulation now for the second time and the behavior is
always the same. Has anybody an idea what happens there? I attached
plots of the total temperature and energy.
have you looked at what actually happens to the structure of your
system? what you describe sounds a lot like you have a phase transition
happening, e.g. freezing water or something similar.
cheers,
axel.
Axel's suggestion is a good one - viz your system.
It could be the classic flying icecube - your system has
frozen and is drifting with a mean velocity. You could
also monitor the center-of-mass drift with fix com.
Steve