Dear GROMACS community, I performed umbrella sampling study to estimate the binding free energy between a globular protein with 568 residues and a small peptide with 13 residues. I use the pull code with k = 800 and rate = 0.005 to generate the initial conformations over the time course of 1200 ps. The center of masses distance between the pull groups ranges from 1.4 nm ad 7.8 nm in the pull trajectory.
I then extract conformations from pull.xtc with a spacing of 0.1 nm until 3 nm distance and a spacing of 0.2 nm for the remainder, yielding 38 windows in total. After having equilibrated each window with NVT and NPT under full position restraints, I conducted production simulation under NPT ensemble for 14 ns for each window. Finally, gmx wham computed the PMF curve which you can see here: https://www.dropbox.com/s/fp7ol41qoyokmjm/profile.xvg?dl=0 and this is the associated histogram: https://www.dropbox.com/s/bp6obymjc2qeu37/histo.xvg?dl=0 Please find here my MDP pull parameters: pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = chainB ; Protein pull_group2_name = chainC ; Peptide pull_coord1_type = umbrella pull_coord1_geometry = distance pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_rate = 0.0 pull_coord1_k = 800 pull_coord1_start = yes I would now be very interested why the curve does not become flat beyond some certain distance, but rather seems to increase in a linear fashion, though the distance between the pull groups is sufficiently large. Could this be related to entropic effects? Is there a way to have the PMF properly normalized? The force field here is GROMOS 53a6 with SPC water. Temperature is coupled to 310 K and pressure to 1 bar. Cutoffs are 1.4 nm, longe range ES are resolved with PME and DispCorr is set to EnerPress. Bonds are constrained with LINCS. The Protein is prevented from rotation by having three CA atoms restrained with FC 1000. Thank you very much, I appreciate any help and suggestions. Lukas -- 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.
