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 <jalem...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
