On 12/19/13 5:47 PM, rdwducl wrote:
Hello, I am using GBSA/OBC implicit solvation with an ACE-type approximation for the nonpolar term. Having looked at the GROMACS code, it would appear to be using the following form for the nonpolar free energy: sum_i 4*pi*tension*(R_i + R_s)^2 * (R_i/b_i)^6 where R_i and R_s are constants (vdw and probe radii), and b_i is the conformation-dependent Born radius. The idea is that as solutes come together, b_i increases and so the free energy decreases. To test this effect, I have written a script that iteratively creates configs with the 7 atoms (of type "CH2"): (0,0,0) (r,0,0) (-r,0,0) (0,r,0) (0,-r,0) (0,0,r) (0,0,-r) and then computes the GB nonpolar energy as a function of r in [0.1,1.0] nm. What I'm finding is a /constant/ nonpolar energy, i.e. it is not varying with r! My input files are below. Am I doing something wrong?
You have 7 atoms that have no bonded geometry, so no matter where you place them, the exposed area is constant.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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.