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

[lazaro monteserin]

Dear Dr. Lemkul you are completely right. But then how could I approach
this problem to get an answer at the end that make sense?

On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/18/20 7:39 PM, lazaro monteserin wrote:
> > 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?
>
> How do you propose to compute the conformational free energy? Note also
> that no biomolecular force field is validated for use in the gas phase,
> so the balance of conformational sampling has no guarantee of being
> physically meaningful.
>
> > 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.
>
> You can enforce dihedral rotation with the pull code, but the tutorial
> has little use here aside from general concepts.
>
> > 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.
>
> The tutorial is for decoupling a solute from water. You have a molecule
> in vacuum. The only thing to decouple is the molecule itself, which will
> give you an annihilated, physically nonsensical structure.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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