[gmx-users] PMF steadily increasing

Mon Jun 20 12:04:00 CEST 2016

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.zim91 at 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.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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