[gmx-users] thermostate

hosein geraili geraili_hosein at yahoo.com
Wed Nov 28 09:24:35 CET 2018

How can I get the temperature of a certain group from .edr or .trr, like the gmx energy, but the problem with gmx energy is, it just gives the temperature for the whole system.
Another question is, do you think it makes sense to use a thermostat with a coupling constant of 100 ps for a very long run (microsecond) on a protein to study its dynamic quantitatively?? Or is it better to use just the coupling on the solvent and not protein??
Also, Is it just GROMACS that have the ability to assign the thermostat to different groups with a different coupling constant?? I mean, it is a very hard decision, and it adds up to my doubt about not using the thermostat on protein and just on solvent when I see that AMBER MD engine doesn't even have the option to assign different coupling constant to different groups.

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