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

[Justin A. Lemkul]

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
>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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