[gmx-users] Re: umbrella sampling with "pull=constraint"

[Vijayaraj]

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
> Subject: [gmx-users] umbrella sampling with "pull=constraint"
> To: gmx-users at gromacs.org
> Message-ID: <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.
>
>
>
> -
>
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