[gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti)

Christopher Neale chris.neale at alum.utoronto.ca
Sun Jul 26 04:45:58 CEST 2015

Dear Eudes:

Glad that you solved one of the two issues. As for the bumps in the PMF, I have a new theory: the bumps come from pressure coupling. When the sampled distance, d, between the two molecules fluctuate a little closer than the center of restraint, d0, that adds a repulsive force that contributes to the virial and the box gets a little larger. Conversely, slight fluctuations of d that are larger than d0 will add a small bias to box contraction. This should be more noticeable when the restrained distance involves larger masses.

It is at the moment unclear to me whether this might exert an effect indirectly due to overall system density or more directly as coordinate scaling impacts the instantaneous value of d. If it is the latter, then semi-isotropic pressure coupling, may also enhance the effect since the virial will be computed independently along the order parameter (I presume) and hence there is less noise from other dimensions.

Can you please try again without pressure coupling (single precision should be fine for this test). Hopefully this is not the source of the bumps because, if it is affecting the PMF noticeably and the underlying free energy surface has a large gradient, then d will always be on one side of d0 and the effect will not be merely bumps but also some type of bias in the PMF. Whether this bias is accurate or artifactual falls outside of my mathematical abilities. The thing is, the force is a real force between real atoms so it seems like it really should be included in the virial (as it certainly is... I checked). I can tell you one thing for sure: the effect on box volume is real and noticeable. That is, if you look at the average system volume when d<<d0, it differs in a statistically significant manner from the average system volume when d>>d0 (something that I also checked).

Thank you for looking into this further,

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Eudes Fileti <fileti at gmail.com>
Sent: 24 July 2015 16:47
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes     Fileti)

Hello Chris, I write to report the results of the tests you suggested.
To recap, I have two problems to solve. 1) The bad sampling around z = 0
and 2) the bumps along to the profile.

I solved the first discarding all the my initial configurations and
performing a new pulling (SMD). Only this time I used a higher force
constant (5000 kJ/mol nm2). Thus I got configurations close to z = 0, where
they were not generated.

For the second problem, you suggested recalculate the PMF using double
precision. The results of this test showed that it does not solve the
problem, on the contrary the bumps were even more pronounced, as indicated
by the plot in this link. https://goo.gl/photos/wGNhdyNG9pdqGfcB6

All tests were performed with prototypes simulations, with 40 windows of 2
ns spaced by 0.1 nm. A larger sample is obviously necessary for reliable
profiles, but this was enough to show the trend that I wanted to watch.

As I have mentioned before, I've done several tests aiming to eliminate
these bumps: use of higher sampling, up to 20ns per window; reducing the
spacing between the windows (from 0.1 to 0.05 nm); changing the spring
constant from 1000 up to 5000 kJ/mol nm2, use of two different versions of
the Gromacs (4.6 e 5.0) and also I tested it with two different sets of
initial settings.

None of this attempts solved the bumps problem.

If you (or someone else) have any other tips please let me know.

Thank you

Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Página: sites.google.com/site/fileti/

> ------------------------------
> Message: 4
> Date: Wed, 22 Jul 2015 14:56:50 +0000
> From: Christopher Neale <chris.neale at alum.utoronto.ca>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> Message-ID:
>         <
> BLUPR03MB18470A33A4E3FF149C95963C5830 at BLUPR03MB184.namprd03.prod.outlook.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
> Dear Eudes:
> There are two issues: The first issue is the fact that you've got a
> sampling problem near the bilayer center. The second issue is the periodic
> bumps that you see in your PMFs. I'll take the second part first.
> The source of the periodic bumps in PMFs from umbrella sampling is, to me,
> a million dollar question. I've seen them in my own work. I've seen then in
> the literature (as you noted for Fig. 4 in
> http://www.mdpi.com/1422-0067/13/11/14451/htm ). I've seen them when
> people use g_wham and Alan Grossfield's version of WHAM. What I don't yet
> know is if people also see this when running US simulations with AMBER,
> CHARMM, or NAMD. Frankly, either answer scares me a little. If you see wild
> oscillations of the PMF, at large distances then one possible source is
> that you are near a distance that is half your box length along the order
> parameter. Note that with constant pressure simulations you will get
> oscillations in the length of the box and also when your membrane changes
> shape it could flip the vector of closest approach by 180 deg if you are
> close to the half-box limit. However, that should not be relevant to the
> bumps (out of interest, how large is your box along z?). Although I do
>  n't know what is going on with these PMF bumps, I also note that
> membranes as a whole always tend to migrate toward positive z and lipids
> tend to flow to positive x in gromacs simulations, so I wonder if it is a
> rounding issue. Could you try again with double precision and see if you
> get the bumps?
> As for the problem with sampling near the bilayer center... my first guess
> is that you've got some of your replicas on the wrong side of the bilayer's
> center. Did you intend to go across the center and sample also in the lower
> leaflet? I've only ever used gromacs 3 and 4 to do pulling simulations,
> never gmx 5. You can see my concerns about gmx5 for this type of issue near
> the bilayer center here:
> https://www.mail-archive.com/gromacs.org_gmx-users%40maillist.sys.kth.se/msg11324.html
> One simply has to test it. However, if gmx5 does indeed work properly with
> this new US philosophy, then I presume that you simply need to move your
> starting coordinates such that your solute is in the positive leaflet for
> all replicas. You can test this by visualization or g_dist, which reports
> the sign of the displacement (look in the 5th column I think for the z
> value). Note that you are using pull_start=yes, so which side of the
> bilayer your solute is initially on should make a difference here.
> Chris.
> -- original message:
> Hi Chris, a few days ago I posted a question on GMX list but unfortunately
> I not received an answer yet. So I write to you for help at your
> convenience.
> http://permalink.gmane.org/gmane.science.biology.gromacs.user/78439
> Besides the problem exposed the link above I'm trying to understand the
> importance of the relative distance between the COM. Due to fluctuation in
> the position of the center of mass position of the membrane, the minimum
> distance is never zero, as shown in the graphs of my pulling below. What is
> the effect of this difference in the calculation of the PMF? Could this be
> the source of my problem?
> https://goo.gl/photos/cwwLzog6wXAgVJG88
> Bests
> eef
> PS. I found this paper below where authors have published this unusual
> behavior (Figure 4). They did not explain the reason for the oscillations
> at large distances and I also do not know why this occurs.
> http://www.mdpi.com/1422-0067/13/11/14451/htm
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Eudes
> Fileti <fileti at gmail.com>
> Sent: 18 July 2015 21:06
> To: gmx-users at gromacs.org
> Subject: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> Hello guys, I'm trying to calculate the PMF using umbrella sampling for a
> small molecule to penetrate a lipid membrane. The 1D reaction coordinate is
> along the z axis, which corresponds to the bilayer normal. The umbrella
> potential acts on the center of mass of the molecule. The initial
> configurations for each window, separated by a distance of 0.1nm, in a
> range of 4 nm (distance between the centers of mass of the membrane and the
> molecule), were obtained by a SMD.
> The umbrella potential was applied according to the parameters below (for
> Gromacs version 5.0.3). Each window was sampled by 5 ns.
> pull                     = umbrella
> pull_geometry            = direction
> pull_dim                 = N N Y
> pull_start               = yes
> pull-print-reference     = no
> pull_nstxout             = 1000
> pull_nstfout             = 1000
> pull_ngroups             = 2
> pull-ncoords             = 1
> ; Group name, weight (default all 1), vector, init, rate (nm/ps),
> kJ/(mol*nm^2)
> pull-group1-name         = DPPC     ;  ref
> pull-group2-name         = LIG         ;  pulled
> pull-coord1-groups       = 1  2
> pull-coord1-origin       = 0 0 0
> pull-coord1-vec          = 0 0 1
> pull-coord1-init         = 0
> pull-coord1-rate         = 0.0
> pull-coord1-k            = 3000
> Histograms and the PMF obtained are shown in figure the link below.
> https://goo.gl/photos/RkW9gbWrgeKEfV3R7
> I repeated the same test using other parameters (larger and small k values)
> and options (cylinder and position, for this later I have used gmx 4.6) and
> so far I could not get a satisfactory profile. In all tests, a problem that
> I have observed is that the region near z = 0 is not sampled (there is a
> gap between 0.0 and 0.5 nm). In addition the profile presents not smooth,
> but somehow oscillating mainly for large z.
> As the gmx distance give a value different of zero for the smallest
> distance of separation between the centers of mass (around 0.1-0.2 nm) I
> believe that this weird behavior is related to the reference distance that
> I have used.
> Could someone give me a light? Most of the tips I read in GMX list are
> related to previous versions of the Gromacs and in a way the other tips
> were already included in my tests.
> Thank you
> eef
> _______________________________________
> Eudes Eterno Fileti
> Instituto de Ci?ncia e Tecnologia da UNIFESP
> Rua Talim, 330, S?o Jos? dos Campos - SP
> P?gina: sites.google.com/site/fileti/
> --
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