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

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Jan 6 17:12:38 CET 2012

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?
By free I mean. The absolute distance between the COG of the ref group
and that of the pull group.



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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