Dear Dr. Lemkul thank you very much for your answer. I will look on the literature.
El lun., 13 de abr. de 2020 a la(s) 12:55, Justin Lemkul (jalem...@vt.edu) escribió: > > > On 4/13/20 10:37 AM, lazaro monteserin wrote: > > 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? > > Freezing and restraining are different; don't use the terms > interchangeably. Freezing means the atoms are never updated (position or > velocity), and I don't recommend using this approach as it is entirely > unphysical. What you're talking about is applying a restraint. You need > to assign all atoms to a temperature-coupling bath. If you don't, that's > also completely unphysical. > > > 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? > > For a small solute in water, couple the whole system together. > > > 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? > > You should base this conclusion on your examination of the literature. > What are the time scales of the dynamics you are interested in? What > have previous studies on similar systems demonstrated? > > -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.