[gmx-users] Re:umbrella sampling with "pull=constraint"

Thomas Schlesier schlesi at uni-mainz.de
Mon Nov 7 15:07:11 CET 2011

If you use constraints it would not be umbrella sampling, where you need 
to sample around a restraint structure to get the histograms for WHAM or 
another analysis-technic.
So if you want to do umbrella sampling either make to box bigger and/or 
make the restraints harder.

But you can also use constraints instead of restraints. But it would 
require another analysis-technic. Think it's called thermodynamic 
integration. In the end you also sample many different windows with 
varying distances, but instead of using WHAM you integrate the 
constraint force to obtain the PMF.


One important thing to note is, that you will need more windows compared 
to umbrella-sampling, since in each window you sample only on distance 
and not around one distance (restrains allow for a change of the distance).

Another thing to note is the pull_dim. For determining the PMF of an 
end-toend distance of similar i would turn all three dimensions to 'yes'.
Imagine to parallel sheets of paper, with z perpendicular to the papers. 
With your setup you would only fix the z-distance between both sheets, 
but they can move freely in the xy-plane.

Hope that helps.

> Hello,
> I have done umbrella sampling with "pull=umbrella" and I found that the
> pulling group has high fluctuations and sometimes moving out of the
> periodic box. I think that the harmonic potential is not properly applied
> and thus the pulling group is not retained with the specified COM distance
> between the reference and pulling group. Can we use pull=constraint option
> to retain the pulling group within the COM distance? my pulling code is as
> bellow with restrain at 0.5nm distance from ref group. I just want to get
> some idea about this pull code modification.
> pull            = constraint
> pull_geometry    = distance
> pull_dim        = N N Y
> pull_start      = no
> pull_ngroups    = 1
> pull_group0     = Chain_A
> pull_group1     = Chain_B
> pull_init1      = 0.50
> pull_rate1      = 0.0
> pull_k1         = 1000
> pull_nstxout    = 500
> pull_nstfout    = 500
> Regards,
> Vijay.

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