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. Is there any other parameter which decides the number of scaling atoms and/or to modify the scaling factor to acheive target temp.? Prasad MVD.

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

Hi everyone, recentely I did a simulation work on the incipient yield surface of nano-voided single crystal Cu, in [100]-[010]-[001] crystalline system. Together with the size effect on yield strength studied, the macroscopic incipient yield surface for Cu is expected to be predicted. Also, I try to build the relation between the loading modes and failure pattern, but I really don't understand the defected atomistic pattern clearly. So any suggestion or discussion on this part would be appreciated. Thank you for attention. Detailed description seen in attachment file.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
the Newtonian equations of motion for systems with hundreds to millions of
particles.

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.