[gmx-users] PMF steadily increasing

[Lukas Zimmermann]

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.neale at 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-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
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