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.
