Thank you very much for your suggestions. I will check your individual remarks and provide feedback.
2016-06-15 19:01 GMT+02:00 Christopher Neale <chris.ne...@alum.utoronto.ca>: > (1) Are the protein and peptide really never interacting at d=7 nm? I > presume you've got a peptide that would be maybe 5 nm long when fully > extended, and your dG minimum is at 1.5 nm, so giving half the peptide > length that would imply possible contact at 4 nm, so I expect 7 nm is > sufficient, but gmx mindist can tell you for certain. For example, if the > protein forms an overhanging pocket around the binding site, then it is > quite possible that an unfolded peptide would be sometimes (even rarely) > contacting a 568 residue protein even at a COM-COM distance of 7 nm. > > (2) net charge positive on one and negative on the other? > > (3) unconverged? Did you try eliminating the first half of your production > sampling and see if this fixes the issue? > > (4) did you do wham properly? Your mdp file indicate that your windows are > not *exactly* at 0.1 and 0.2 nm increments (use of pull_coord1_start=yes), > which is fine but only as long as wham doesn't think your windows are > exactly at these increments. > > There may be some entropy change as the peptide becomes unbound and can > then sample full X and Y, but on its own that should not continue to impact > the sampling after contact is permanently broken. > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Lukas > Zimmermann <luk.zi...@gmail.com> > Sent: 15 June 2016 12:45:51 > To: gmx-us...@gromacs.org > Subject: [gmx-users] PMF steadily increasing > > 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. > -- > 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. > -- 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.
