Ensemble choices for MSD calculation

Hi,

Temperature you studied is rather high, please check effect of time step.

  1. Use fix temp/rescale with fix NVE to control the temperature precisely. But I learned from mail-list that this is not usually recommended.

–>> Yes, should not use this fix when study the transport properties (You can find some discussions in some text books, such thermostat does not discribe the system in true NVT ensmble). Try to test “fix langevin”
2. Use fix NVT to calculate MSD rather than fix NVE. It may require a bigger Tdamp to decrease temperature fluctuation.
–>> Should use NVT, but check effect of time step and Tdamp.
In fact, you can also use NPT… Results are similar.

Best,

Hi,

Temperature you studied is rather high, please check effect of time step.

1. Use fix temp/rescale with fix NVE to control the temperature precisely.
But I learned from mail-list that this is not usually recommended.
-->> Yes, should not use this fix when study the transport properties
(You can find some discussions in some text books, such thermostat does not
discribe the system in true NVT ensmble). Try to test "fix langevin"
2. Use fix NVT to calculate MSD rather than fix NVE. It may require a
bigger Tdamp to decrease temperature fluctuation.
-->> Should use NVT, but check effect of time step and Tdamp.
In fact, you can also use NPT... Results are similar.

for correct MSD calculations, a weakly coupled thermostat is needed, and
then ​the fluctuations ​with either fix nvt or fix nve should be of
comparable magnitude. if they are not, then you don't have a weakly coupled
thermostat and thus the thermostat settings should be adjusted accordingly
or there are some general problems with the equilibration workflow, that
need to be addressed. there is not enough information to tell which is
happening. the "natural" magnitude of temperature fluctuation depends on
(as mentioned) the temperature, the strength of the interactions and the
size of the system.

axel.