[gmx-users] Temperature coupling of two-phase system

[朱文鹏]

Dear Gromacs users,

I am trying to simulate nanotube-based channel (CNT: 3872 carbon atoms)
with water (SOL: 15758 H2O). The nanotube is position restrained during
simulation, while water molecules are constrained by . I've used two kinds
of tc-grps setting. One is "tc-grps = System". The other is "tc-grps = CNT
SOL". For both cases, I calculated temperatures of each group by using
g_traj. They were corrected by accounting the degrees of freedom (DOF) of
CNT (5805) and SOL (94545). However, I am confused about the temperature
results and not sure which one is correct.

For the "tc-grps = System", the temperature of water is reported to be 300K
as I expect. But the CNT temperature fluctuates around ~66K. It is much
lower than the target temperature. I think it is caused by the huge
difference of atom numbers and mass between CNT and SOL. Is it correct?

For the case of "tc-grps = CNT SOL", the temperature coupling is more
accurate. The temperatures of both groups can reach the target temperature
(300K). But I am told that such a thermostat for every component separately
is unrealistic.

I wonder which tc-grps setting I am supposed to use for temperature
coupling. tc-grps = System, tc-grps = CNT SOL, or even tc-grps = SOL only
(it is like using 300K water to warm up CNT). I would appreciate it if you
have any suggestion.

Thank you very much for your attention.

Best,
Jason