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

[Gavin Melaugh]

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?

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
>