# [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
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
>>>
>>>> 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
>>>>      >>>>  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,
>>>> 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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