[gmx-users] using one thermostat for entire system ??

Jennifer Williams Jennifer.Williams at ed.ac.uk
Mon Mar 7 16:50:01 CET 2011


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?



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