Thank you again for your remarks. This is what I found so far: (1) With gmx mindist it was very clear that protein and peptide do not interact. For the last 5 or 6 Umbrella Windows, the minimal distance between the Pull groups was at least 2 nm (2) That is indeed the case. The protein has net charge -1 and the peptide has charge +3. Can you tell me what effect this might have? I am unaware that this might cause problems. (3) I tried this, but this showed no apparent effect on the shape of the curve. (4) I do not understand in how far WHAM cares about the COM-COM distances. I extract my frames from pull.xtc and I do not see each COM-COM distance that would be required to have exactly, say, 0.1 nm spacing, so I use a script which selects frames which resemble 0.1 nm spacing as closely as possible, so there might some deviation.
2016-06-16 21:24 GMT+02:00 Lukas Zimmermann <luk.zi...@gmail.com>: > 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.
