[gmx-users] RDF(PMF) and Umbrella sampling
Thomas Schlesier
schlesi at uni-mainz.de
Tue Jan 10 12:20:41 CET 2012
I think that for the histogram all contribution with a negative sign
would be add to the contributions from positive distances. If your
distribution is be a perfect gaussian with zero mean, you would end up
with half a gaussian with double high (for positive distances) and zero
for negative distances. For this case it would be easy to correct the
histogram. But if the histogram isn't a perfect gaussian, you couldn't
say anything.
> Date: Tue, 10 Jan 2012 10:47:43 +0000
> From: Gavin Melaugh<gmelaugh01 at qub.ac.uk>
> Subject: Re: [gmx-users] RDF(PMF) and Umbrella sampling
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Message-ID:<4F0C174F.2050901 at qub.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Justin
>
> Again, many thanks for the reply.
> So when the COM distance changes sign, what effect does that have on the
> distribution of the COM distance about the mean value for that window
> i.e. If say my ref dist in 0 nm and the umbrella sampling allows the
> distance to sample distances say at 0.02 nm to -0.02nm. What happens to
> negative values? Obviously they are not counted as negative in the
> distribution or else it would be centred at zero/
>
> Cheers
>
> Gavin
>
> Justin A. Lemkul wrote:
>>
>>
>> Gavin Melaugh wrote:
>>> Hi Justin
>>>
>>> Thanks very much. One last question. What do you mean when you say "COM
>>> reference distance is changing signs"? I thought the COM distance was
>>> the absolute distance between the two groups and therefore cannot be
>>> negative?
>>>
>>
>> The pull code deals in vectors. Signs can change. The use of
>> "distance" as a geometry is perhaps somewhat misleading.
>>
>> -Justin
>>
>>> Cheers
>>>
>>> Gavin
>>>
>>> Dariush Mohammadyani wrote:
>>>> Hi Gavin,
>>>>
>>>> A question arose for me: why did you consider the (rate = 0)?
>>>>
>>>> Dariush
>>>>
>>>>
>>>> On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh<gmelaugh01 at qub.ac.uk
>>>> <mailto:gmelaugh01 at qub.ac.uk>> wrote:
>>>>
>>>> Hi Justin
>>>>
>>>> Just a quick clarification regarding my previous point. With
>>>> geometry =
>>>> distance, and pull_dim =Y Y Y . Is the pull_group sampling all
>>>> dimensions equally (or without prejudice) about pull_init ? And
>>>> iN your
>>>> first reply what did you mean about by "straight pull" ?
>>>>
>>>> Cheers
>>>>
>>>> Gavin
>>>>
>>>> Justin A. Lemkul wrote:
>>>> >
>>>> >
>>>> > Gavin Melaugh wrote:
>>>> >> Hi Justin
>>>> >>
>>>> >> Thanks for the reply. I wanted my "pulling" to be free in all
>>>> >> directions, that is in the liquid state with no defined reaction
>>>> >> coordinate i.e not along a specific axis. This is why I used
>>>> geometry =
>>>> >> distance. Would you agree with this approach?
>>>> >
>>>> > I suppose there is an argument that can be made for a more free
>>>> > approach such as this one, but you're going to get the
>>>> artifact you
>>>> > observed the instant your pull group moves past a zero COM
>>>> distance.
>>>> > Whether or not this is a significant problem is something you'll
>>>> have
>>>> > to determine.
>>>> >
>>>> > -Justin
>>>> >
>>>> >> By free I mean. The absolute distance between the COG of the
>>>> ref group
>>>> >> and that of the pull group.
>>>> >>
>>>> >> Cheers
>>>> >>
>>>> >> Gavin
>>>> >>
>>>> >> Justin A. Lemkul wrote:
>>>> >>>
>>>> >>> Gavin Melaugh wrote:
>>>> >>>> Dear all
>>>> >>>>
>>>> >>>> I have a query regarding umbrella sampling simulations that I
>>>> have
>>>> >>>> carried out to study a dynamical process of a guest inserting
>>>> into a
>>>> >>>> host. I always get get a wall tending off to infinity at or
>>>> just
>>>> >>>> before
>>>> >>>> the zero distance between the
>>>> >>>> two species.
>>>> >>>> The process I describe, for one system in particular, happens
>>>> readily
>>>> >>>> and I have compared the PMF from a non constrained simulation
>>>> (via the
>>>> >>>> RDF and reversible work theorem) and the same PMF from a
>>>> set of
>>>> >>>> umbrella sampling
>>>> >>>> simulations. They agree quite well but in the non constrained
>>>> >>>> simulation
>>>> >>>> I get a minimum practically at zero whereas for the umbrella
>>>> sampling
>>>> >>>> the minimum is shifted and there is an infinite wall close to
>>>> zero.
>>>> >>>> This
>>>> >>>> wall is not present from the reversible work theorem. Why the
>>>> infinite
>>>> >>>> wall? Why does the black histogram not centre around zero. Is
>>>> this an
>>>> >>>> artefact of the umbrella technique? Please see attached the
>>>> profile
>>>> >>>> from
>>>> >>>> the umbrella sampling technique, and the corresponding
>>>> histograms.
>>>> >>>>
>>>> >>> What's happening is the COM reference distance is changing
>>>> signs, so
>>>> >>> you get an artifact. The "distance" geometry is relatively
>>>> inflexible
>>>> >>> and is only suitable for straight pulls of continuously
>>>> increasing or
>>>> >>> continuously decreasing COM distance. You should try using the
>>>> >>> "position" geometry instead. There are some notes that you
>>>> may find
>>>> >>> useful in my tutorial:
>>>> >>>
>>>> >>>
>>>>
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html
>>>>
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>> -Justin
>>>> >>>
>>>> >>>> Here is an excerpt from one of the umbrella mdp files.
>>>> >>>>
>>>> >>>> pull = umbrella
>>>> >>>> pull_geometry = distance
>>>> >>>> pull_dim = Y Y Y
>>>> >>>> pull_start = no
>>>> >>>> pull_ngroups = 1
>>>> >>>> pull_group0 = cage_1
>>>> >>>> pull_group1 = tail
>>>> >>>> pull_init1 = 0
>>>> >>>> pull_rate1 = 0.0
>>>> >>>> pull_k1 = 10000
>>>> >>>> pull_nstxout = 150
>>>> >>>> pull_nstfout = 150
>>>> >>>>
>>>> >>>>
>>>> >>>> Cheers
>>>> >>>>
>>>> >>>> Gavin
>>>> >>>>
>>>> >>>>
>>>> >>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> >>>>
>>>> >>>>
>>>> >>>>
>>>> >>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> >>>>
>>>> >>>>
>>>> >>
>>>> >>
>>>> >
>>>>
>>>> --
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>>>>
>>>>
>>>>
>>>> --
>>>> Kind Regards,
>>>> Dariush Mohammadyani
>>>> Department of Structural Biology
>>>> University of Pittsburgh School of Medicine
>>>> Biomedical Science Tower 3
>>>> 3501 Fifth Avenue
>>>> Pittsburgh, PA 15261
>>>> USA
>>>>
>>>
>>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 10 Jan 2012 10:54:19 +0000
> From: Steven Neumann<s.neumann08 at gmail.com>
> Subject: [gmx-users] Energy Minimization
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Message-ID:
> <CAKZJqQGcXR6PqJemePfjiVU8+y_qn3BgMqM6JF3wKsK48UvpPQ at mail.gmail.com>
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>
> Dear Gmx Users,
>
> I am setting up my simulations of carbon tube with protein. I solvated my
> system, added ions and I would like to run EM of my system. My carbons of
> the tube in MD will be restrained. In this case should I run EM of my
> protein in water (and with ions) separately and the copy coordinates and
> then process with NVT and NPT or run EM with restrained nanotubes of my
> system directly?
>
> Thank you,
>
> Steven
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