Dear All,
Recently I have read some literatures on Molecular simulation of polymer. My interest is measurement of
mechanical properties of polymer through the uniaxial tensile test.
I have a question about relatively large time scales in MD simulations of polymer and how to interpret MD
stress-strain results for FE modeling. In particular, in the literature it is mentioned that strain rate of
I am trying to apply Berendsen thermostat for CNT. When I choose to leave one third of the tube atoms to evolve freely with out distrubing the momentum, I am unable to acheive the target temperature and further temperature increases gradually over the whole simulation run (even with a thermostat parameter equals to the timestep i.e., like a simple scaling). How it is possible to acheive target temperature,by scaling only a part of atoms, using some scaling value which should actually scales all the atoms momenta.
Hi, all
Molecular dynamics (or MC) is a powerful tool in the protein research. There're lots of scientific works in this field, which deepen our understanding gradually. My question follows, "how about the continuum mechaics in protein research".
Any discussions and advices are appreciated.
Kong 5th Sep 2007
Calculating stresses in MD simulations is a controversial topic. There are two different schools of thought about the equivalence of the virial stress to the continuum Cauchy stress; for and against. Some argue based on momentum balance, that only the potential contribution to the virial stress should be considered as the continuum Cauchy stress. However, others assert that the total virial stress that contains both the kinetic and potential parts is indeed the quantity that corresponds to the Cauchy stress in continuum mechanics. We used a simple thermo-elastic analysis to verify the validity of using the total virial stress as the continuum Cauchy stress and found that the total virial stress is indeed the continuum Cauchy stress.
