On 4/13/18 2:22 AM, rose rahmani wrote:
Hi, I have 2 questions, but please consider them 2 distinct questions and are not related. I did umbrella sapmling and calculate the PMF. Now i I want to calculate number of hydrogen bonds for amino acid in its initial distance(far from surface) and binding distance ( which is close to surface and PMF is minimum there). 1- Is it rational to use pulling data(traj.xtc, .tpr,...) to calculate this analysis, as it is nonequilibrium condition?
Sure. In each umbrella sampling window, you're restricting motion along a reaction coordinate, which allows you exactly compute distance-dependent properties.
2- Is it better to choose initial frame and binding frame, do umbrella sampling step (, nvt) and calculate number of hbons separately and compare the result? Is it true to compare them in this condition?
Using only the starting frame makes no sense. There's no reason to think that any single frame from any simulation is representative of the actual ensemble.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.
