> It means to evaluate quantities over successive blocks of time (e.g. using -b > and -e that all GROMACS analysis tools support) and check to see whether or > not the quantities of interest are varying over time or if they are stable, > i.e. converged.
Thank you, Justin. What size of blocks I need to divide in such an analysis? e.g., for a 100-ns trajectory, is it appropriate to divide it into 5-ns or 10-ns blocks to see if it has converged? Qing At 2015-07-10 01:39:42, "Justin Lemkul" <[email protected]> wrote: > > >On 7/9/15 10:11 AM, Qing Lv wrote: >> 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... >> > >If you are hypothesizing a conformational change, then you need a way to >quantify that change - distances, angles, etc. > >> Could you give me more info on block-averaging, or any other advice that >> will help? >> > >It means to evaluate quantities over successive blocks of time (e.g. using -b >and -e that all GROMACS analysis tools support) and check to see whether or >not >the quantities of interest are varying over time or if they are stable, i.e. >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 > >[email protected] | (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 [email protected]. -- 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 [email protected].
