Are you sure that you have sampled all the windows in your grid? In a 1D
scenario, let's say you needed 20 windows for a distance constraint, and
then you want to add in an angular constraint which would also have 20
windows if it was run as a 1D on its own, then you now need to setup and
run 20x20=400 different simulations to get all the windows. If you are
getting harmonic looking plots, it sounds to me as though you haven't made
all the windows, and so for some of the 1D slices of your 2D PMF, you are
just seeing the results of using WHAM with a single window.
Otherwise you might test it quickly using the ABMD module, which I think
easily supports multiple dimensions and could at least give you a rough PMF
to gauge any problems. According to the manual you can also use this rough
PMF as a bias for future umbrella sampling to speed things up, but I've
never tried this.
~Aron
On Tue, Feb 28, 2012 at 10:30 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> have you looked carefully at your distance vs time plots, BEFORE you
> feed them to wham?
>
> Make sure that your distances are actually close to the distance you
> requested in your restraint files.
>
> Adrian
>
>
> On 2/28/12 10:28 AM, Sampson C.M. wrote:
> > Hello,
> >
> >
> >
> > I am trying to use Umbrella sampling with WHAM to generate a 2D PMF. If
> I use 1 constraint the PMF comes out looking reasonable, as soon as I add
> anymore restraints I get strange results, e.g. straight lines or harmonic
> shaped curves
> >
> >
> >
> > Is it possible to use multiple constraints to generate a 2D PMF?
> >
> >
> >
> > Thanks
> >
> >
> >
> > Chris
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Feb 28 2012 - 10:00:03 PST
