Hi,
I simulated the diffusion of small gases (CO2, N2) in a framework
structure which was mostly frozen with some mobile surface groups. I
applied a temperature thermostat to the entire system (i.e I didn't
couple the gas molecules and framework separately). I have now been
asked the following by a reviewer:
"Please comment on any artefacts that might arise as a result of
non-equipartition of energies. For example, what is the calculated
temperature of each of the gas species and mobile species?"
I have tried to explore the temperature of each species separately but
g_energy will only give me the energy of the system as a whole. Are
there any other tools within gromacs to look at the temperature of
each species in turn from the md runs I already have?
Does anyone have a suggestion as to how I can address the reviewer's
comment and proove that using one thermostat for the whole system is
OK (that is what I am hoping!). Is there anything in particular that
I should be looking closely at?
Thanks
Jenny
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