On 4/5/20 7:13 AM, Quyen V. Vu wrote:
Dear Justin, In your tutorial, you selected the initial configuration for each umbrella by the radial distance between chain A and B [ r = sqrt(x^2+y^2+z^2)] and in umbrella sampling simulation, your setting is: pull_coord1_dim = N N Y pull_coord1_start = yes so as the draw I attached here you can see that conf1,conf2 and conf3 are satisfied the distance criteria and you used the staring z-separation as reaction coordinates, this mean umbrella 1 and 2 will sample the same region while the region between zeta_1 and zeta_3 is not sampled well if |zeta3-zeta1| is large. https://drive.google.com/open?id=1nUKLmaBhjL29ZadgUcPk6DlG08ZVP_Nx Is it true?
Of course it is possible to draw infinitely many configurations that satisfy one dimension but not the total distance.
The tutorial uses COM distance primarily for generating reasonable starting configurations, and over the time scale used, the z-distance and COM distance should not differ much (I proved this to my self 10 years ago when I first wrote the tutorial and did the underlying study). The restraint is applied along z only during the umbrella sampling and that is the reaction coordinate for which the free energy change is computed.
-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.
