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" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
    Subject: Re: [gmx-users] Re: umbrella sampling with "pull=constraint"
    To: Discussion list for GROMACS users <gmx-users@gromacs.org
    <mailto:gmx-users@gromacs.org>>
    Message-ID: <4eb7f727.3000...@vt.edu <mailto:4eb7f727.3000...@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 <vijayara...@gmail.com
    <mailto:vijayara...@gmail.com>
     > <mailto:vijayara...@gmail.com <mailto:vijayara...@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.ne...@utoronto.ca
    <mailto:chris.ne...@utoronto.ca> <mailto:chris.ne...@utoronto.ca
    <mailto:chris.ne...@utoronto.ca>>
     >         Subject: [gmx-users] umbrella sampling with "pull=constraint"
     >         To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
    <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
     >         Message-ID:
    <20111107090721.jy8zfzhvh4ccw...@webmail.utoronto.ca
    <mailto:20111107090721.jy8zfzhvh4ccw...@webmail.utoronto.ca>
> <mailto:20111107090721.jy8zfzhvh4ccw...@webmail.utoronto.ca
    <mailto:20111107090721.jy8zfzhvh4ccw...@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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