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

[Vijayaraj]

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?

On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj <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
>> 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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