Thanks for the reply . I went through the ABMD description .
In my system I want to calculate the potential of mean force between groups
of atoms .I use type=LCOD .
Now for the list i=(1,2,3,4,5,6) does this define distances between 1,2,3
with 4,5,6 . Are there any limitations to maximum number of atoms in the
list.
Kirtana
On Wed, Feb 15, 2012 at 5:43 PM, Aron Broom <broomsday.gmail.com> wrote:
> Hi Kirtana,
>
> I'm not sure what you mean by fixed as I haven't done Umbrella sampling
> with AMBER before, but you certainly don't want to artificially fix it in
> place, as they will affect its degrees of freedom in a manner that is
> independent of the umbrella sampling.
>
> What you should be trying to do, is to apply a harmonic restraint (a
> spring) between say the two alpha-carbons in your residues of interest.
> You will end up having many simulations, each representing a "window" in
> which you step along the distance (going from small to large) while also
> having to potentially change the force constant for the harmonic restraint
> depending on how the system behaves.
>
> You might also want to consider using ABMD (which is outlined in the
> AMBER11 manual) to get a rough but quick idea of what your PMF might look
> like.
>
> ~Aron
>
> On Wed, Feb 15, 2012 at 5:34 PM, kirtana S <skirtana4.gmail.com> wrote:
>
> > Dear Amber Users,
> >
> > I want to do umbrella sampling to obtain the potential of mean force with
> > distance between the residues as the reaction cordinate. The example
> > discussed uses dihedral restraints. Should I use distance restraints by
> > keeping one residue fixed.Please suggest .
> >
> > Thanks
> > Kirtana
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> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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Received on Sat Feb 25 2012 - 22:30:03 PST
