[gmx-users] Temperature Calculation in MD

[Ray Chao]

Hi, gmx users,

I have a questions regarding the temperature calculation during mdrun. The
system is periodic in x and y direction, and there a re two groups of
molecules, polymer and water solvent. The COM motion of the system was
removed in the mdp file. However, each group has its own COM motion. So in
calculating the temperature of each group, e.g, gmx traj, is the COM motion
of each group removed? Or if I want to write my own code to calculate the
temperature, do I need to cal the COM velocity first and then get rid of it?

Thanks for your attention.