[gmx-users] PMF steadily increasing

[Christopher Neale]

(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-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Lukas Zimmermann <luk.zim91 at gmail.com>
Sent: 15 June 2016 12:45:51
To: gmx-users at 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-request at gromacs.org.