[gmx-users] RDF(PMF) and Umbrella sampling

Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Jan 10 12:45:10 CET 2012


Hi Thomas

Many Thanks for the reply. I have attached the histograms I get for the
umbrella sampling. My concern is the black histogram in which I have set
the ref dist to be zero. The distances in the first few windows are very
small as I really wanted this difficult region to be sampled well and
therefore there might be some sampling in the negative distances. Does
the picture here fit with your explanation below ?

Cheers

Gavin

Thomas Schlesier wrote:
> 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
>>>>>      >>>>
>>>>>      >>>>
>>>>>      >>>>
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>>
>>>>>      >>>>
>>>>>      >>>>
>>>>>      >>>>
>>>>>      >>>>
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>>
>>>>>      >>>>
>>>>>      >>>>
>>>>>      >>
>>>>>      >>
>>>>>      >
>>>>>
>>>>>      --
>>>>>      gmx-users mailing list    gmx-users at gromacs.org
>>>>>      <mailto:gmx-users at gromacs.org>
>>>>>      http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>      Please search the archive at
>>>>>      http://www.gromacs.org/Support/Mailing_Lists/Search before
>>>>> posting!
>>>>>      Please don't post (un)subscribe requests to the list. Use the
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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>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> 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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