[gmx-users] Re: umbrella sampling with "pull=constraint"
Justin A. Lemkul
jalemkul at vt.edu
Mon Nov 7 18:38:58 CET 2011
Vijayaraj wrote:
> My system is a self-assembled cyclic peptide, I am trying to extract PMF
> to pull one of the terminal cyclic peptide. I have collected 25 windows
> starting from 0.5nm with 0.05nm window size. the histogram shows up to
> 0.7nm all the windows are overlapped around 0.5nm, and poor sampling
> from 0.6 to 0.75nm. from 0.75nm the sampling is perfect. each cyclic
> peptide has 8 residues and the terminal one forms 8 hbonds with the 2nd
> cyclic peptide. I guess due to this strong hbonding, the sampling window
> up to 0.7nm is very poor. If we extend the simulation only for these
> windows can we get proper sampling windows? this observation is from
> last 10ns of 20ns simulation.
>
It sounds like you need a substantially stronger force constant to restrain the
positions where the sampling is failing.
-Justin
>
> Message: 3
> Date: Mon, 07 Nov 2011 10:20:07 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] Re: umbrella sampling with "pull=constraint"
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4EB7F727.3000504 at vt.edu <mailto:4EB7F727.3000504 at vt.edu>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Vijayaraj wrote:
> > and also I tried to plot the PMF curve from this data, I got few
> warning
> > messages like "no data point in bin 20, You may not get a reasonable
> > profile. Check your histograms!". the histogram shows poor
> sampling from
> > 0.6 nm to 0.7 nm, and the windows in this position completely
> overlaps
> > at 0.5-0.6 nm. should we have to extend the simulation for 0.6-0.7 nm
> > window to get the restrain distance converged?
> >
>
> It is still somewhat difficult to provide any useful advice. You
> haven't stated
> what your system is, how your windows were assembled, at what
> interval they
> exist, or how many you have. The above warnings suggest that you've
> either set
> up the windows wrong, have insufficient data, or are analyzing parts
> of the
> trajectory you shouldn't be (i.e. initial times that are equilibration).
>
> -Justin
>
> > On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj <vijayaraj81 at gmail.com
> <mailto:vijayaraj81 at gmail.com>
> > <mailto:vijayaraj81 at gmail.com <mailto:vijayaraj81 at gmail.com>>> wrote:
> >
> > Hello,
> >
> > Thanks for the suggestions. I did umbrella simulation for
> 20ns and
> > the pull force is as below.
> >
> >
> > 19960.0000 -6.78192
> > 19962.0000 33.3579
> > 19964.0000 -3.1808
> > 19966.0000 -15.0304
> > 19968.0000 -55.4436
> > 19970.0000 -38.9422
> > 19972.0000 -9.41927
> > 19974.0000 -5.95981
> > 19976.0000 0.626319
> > 19978.0000 2.28736
> > 19980.0000 23.5115
> > 19982.0000 10.6415
> > 19984.0000 -0.233446
> > 19986.0000 8.26525
> > 19988.0000 36.7656
> > 19990.0000 26.6017
> > 19992.0000 64.43
> > 19994.0000 53.3844
> > 19996.0000 18.3834
> > 19998.0000 39.8988
> > 20000.0000 43.6291
> >
> > I expect the force should be converged. my understanding might be
> > wrong. I have poor knowledge about this umbrella sampling
> > convergence and image selection for the PMF calculation. is this
> > fluctuation in force due to pulling group motion out of box?
> can you
> > give me some idea about the selection of images for PMF
> calculation?
> > I found from the pullx files that the COM distance converges
> after
> > few ns of simulation. I understood that we cant do PMF study with
> > pull=constraint.
> >
> > Vijay.
> >
> >
> > Message: 2
> > Date: Mon, 07 Nov 2011 09:07:21 -0500
> > From: chris.neale at utoronto.ca
> <mailto:chris.neale at utoronto.ca> <mailto:chris.neale at utoronto.ca
> <mailto:chris.neale at utoronto.ca>>
> > Subject: [gmx-users] umbrella sampling with "pull=constraint"
> > To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > Message-ID:
> <20111107090721.jy8zfzhvh4ccw0ws at webmail.utoronto.ca
> <mailto:20111107090721.jy8zfzhvh4ccw0ws at webmail.utoronto.ca>
> >
> <mailto:20111107090721.jy8zfzhvh4ccw0ws at webmail.utoronto.ca
> <mailto:20111107090721.jy8zfzhvh4ccw0ws at webmail.utoronto.ca>>>
> > Content-Type: text/plain; charset=ISO-8859-1;
> DelSp="Yes";
> > format="flowed"
> >
> > Dear Vijay:
> >
> > Can you please provide evidence for your claim that the
> harmonic
> > potential is not applied properly, since you may decide
> to use
> > pull=umbrella once you have set that up correctly.
> Importantly,
> > movement out of the unit-cell is not a problem, as
> discussed a
> > lot on
> > this list. Nevertheless, you do need to worry about which
> images are
> > used to derive the pulling forces. You can often do that by a
> > judicious selection of pull_pbcatom (read about that
> on-list and in
> > the manual). In some cases, however, pull_pbcatom can not
> assist
> > enough and you are forced to make the box larger. None of
> this is
> > alleviated by pull=constraint, which is why I'm not going
> to answer
> > your question about your .mdp parameters at this point. Let's
> > get the
> > problems identified and solved first with pull=umbrella.
> >
> > Chris.
> >
> >
> > -- original message --
> >
> > Hello,
> >
> > I have done umbrella sampling with "pull=umbrella" and I
> found
> > that the
> > pulling group has high fluctuations and sometimes moving
> out of the
> > periodic box. I think that the harmonic potential is not
> > properly applied
> > and thus the pulling group is not retained with the specified
> > COM distance
> > between the reference and pulling group. Can we use
> > pull=constraint option
> > to retain the pulling group within the COM distance? my
> pulling
> > code is as
> > bellow with restrain at 0.5nm distance from ref group. I just
> > want to get
> > some idea about this pull code modification.
> >
> > pull = constraint
> > pull_geometry = distance
> > pull_dim = N N Y
> > pull_start = no
> > pull_ngroups = 1
> > pull_group0 = Chain_A
> > pull_group1 = Chain_B
> > pull_init1 = 0.50
> > pull_rate1 = 0.0
> > pull_k1 = 1000
> > pull_nstxout = 500
> > pull_nstfout = 500
> >
> >
> > Regards,
> > Vijay.
> >
> >
> >
> > -
> >
> >
> >
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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