[gmx-users] How to heat atoms within a given region and obtain temperture profile

[长只翅膀]

Hi, GROMACS users!


I have looked through Gromacs manual. But I didn't find how to simulate thermal conductivity by NEMD method.  The first problem is how to get a hot region and a cold region by thermostating atoms within a region. In addition, which gmx program could generate data of temperature profile along one direction?


As to the first problem, I know it may need dynamic groups because atoms within a given region will change with time. Does Gromacs support thermostating dynamic groups and which gmx program is responsible for setting those groups? I found gmx select is usualy used for analysis but might not be for this usage.


Could anyone give me some suggestions? Thank you very much!


Sincerely,
Chibang