I thought this approach initially because I will refine the calculations later at DFT level. What do you think?
On Sun, Apr 19, 2020 at 5:17 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/19/20 4:12 PM, lazaro monteserin wrote: > > 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? > > What is the purpose of requiring that the simulation start from the most > stable vacuum conformation? There are very few rotatable bonds in a > nucleoside and they are likely capable of fairly exhaustive sampling in > water, anyway. The force field isn't designed for vacuum so anything you > generate is likely to either be irrelevant in water or otherwise easily > accessible in water in the first place. > > -Justin > > > 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. > >> > > -- > ================================================== > > 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.