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>> 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>
        Subject: [gmx-users] umbrella sampling with "pull=constraint"
        To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
        Message-ID: <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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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