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<gmelaug...@qub.ac.uk>
Subject: Re: [gmx-users] RDF(PMF) and Umbrella sampling
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Message-ID:<4f0c174f.2050...@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<gmelaug...@qub.ac.uk
<mailto:gmelaug...@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.neuman...@gmail.com>
Subject: [gmx-users] Energy Minimization
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Message-ID:
<cakzjqqgcxr6pqjemepfjivu8+y_qn3bgmqm6jf3wksk48uv...@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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