[gmx-users] Queries regarding temperature gradient

[Sabreen Farnaz]

Dear all,

I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be at say
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermostat  (tau_t=-1).
My questions are:
1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with previous
velocities. For production run, I only take the equilibrated structure and
generate velocities again. (No continuation)
Should gen_temp have the same temperature values in each of nvt and md mdp
files?

Please help.
Thank you!

Regards,
Neelima S.