[gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?

[lazaro monteserin]

Dear Gromacs users

I have three questions about the details of running MD of small molecules
in gromacs:

1) If I run a MD in vacuum if I freeze part of the nucleoside (lets say the
carbons in the sugar) with genrestr, should I use temperature coupling
groups?

2) Now, if I freeze in the nucleoside again the carbons from the sugar but
the calculation is in water, should I use temperature coupling?, should I
put the nucleoside in one group and the solvent in another group? What
temperature coupling methodology would be more recommended?

3) For these type of small molecules (around 32 atoms) what would be the
best time to run the MD, e.x. 5ns, 10ns, 20ns, etc?

Kindly,

Lazaro