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

[Dariush Mohammadyani]

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> 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
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