[gmx-users] about correct methodology to run MD of small molecule in gromacs

[lazaro monteserin]

Dear Gromacs users,

As I have referred before I am simulating small molecules (nucleosides)
(around 33 atoms) in vacuum in Gromacs. When I do the simulations at the
end I want to select the most stable structure from the trajectory for the
next steps.

What would be the best methodology to use to run a molecular dynamics for
this?:

1) Run an anneling and collect the different frames for the trajectory and
then at the end analyze the RSMD, free energy and maybe do clustering for
the different frames to select the most stable structure?

2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella
sampling"?, the only problem here is that I want all dihedral angles to
rotate and I do not know how to do this.

3) Do a procedure similar to tutorial 6 "Free energy of solvation" in which
I generate the free energy from different lambda values from consecutive
simulations.

Any suggestions?

I am not sure how to proceed correctly here.

Kindly,

Lazaro