Thank you, Justin. I am trying to simulate a protein-ligand complex to see the conformation transition during the simulation... We propose that the receptor pocket may be subject to a conformational change upon ligand-binding, so I want to verify it by MD... I am really a newbie in molecular simulation and all I did to analysis were time evolution of RMSD, interaction energy, and visualization. I try to do some principal component analysis, but literature said that PCA must be performed after equilibrium...
Could you give me more info on block-averaging, or any other advice that will help? Best, Qing At 2015-07-09 19:41:09, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 7/8/15 9:48 PM, Qing Lv wrote: >> Hi, >> >> I did a 70-ns MD simulation. I wonder how to justify when the trajectory >> reached equilibrium... >> Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns >> and kept stable after that. Could I justify that the system reached >> equilibrium at 12 ns? Are there any methods/criteria to justify the >> equilibrium other than RMSD evolution? >> > >RMSD is pretty useless in telling you anything about convergence. Great, your >structure probably isn't changing a whole lot (but RMSD can also hide >interesting things). Assess convergence based on the quantities of interest - >why did you do the simulation? What behavior are you trying to observe, and >what measurables do you use to assess it? If those metrics are invariant with >time (e.g. via block-averaging or something) then your simulation is likely >converged. > >-Justin > >-- >================================================== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >================================================== >-- >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.
