Suppose I want to move a group of atoms in a specified direction as cannot
specify a representative atoms.
In this situation which would be better for me to use.
Thanks
Kirtana
On Sun, Feb 26, 2012 at 8:46 AM, M. L. Dodson <mldodson.comcast.net> wrote:
>
> On Feb 26, 2012, at 12:05 AM, kirtana S wrote:
>
> > 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.
> >
> >
>
> No. This defines a three distance linear combination:
>
> C1 * |1,2| + C2 * |3,4| + C3 * |5,6|,
>
> where C1, C2, C3 are the coefficients of the combination and |x,y| is the
> distance between x and y. C1, C2, C3 are signed real numbers. LCOD stands
> for "linear combination of distances". Example, proton transfer:
>
> C1 * |donor, H| + C2 * |acceptor, H|,
>
> C1 = 1, C2 = -1. Note H appears in both distances. This collective
> variable
> goes from a negative number to a positive number as the H transfer
> proceeds.
> The CV is 0.0 when the proton is equidistant between donor and acceptor.
>
> Groups of atoms are not allowed in this implementation of LCOD
> (unfortunately).
> There is no hard limitation on the number of atoms (although there must be
> an
> even number of them), but the quality of the statistics falls off with
> increasing numbers of atoms.
>
> Can you determine a "representative" atom in each of the groups? If so,
> use them, maybe?
>
> Good luck,
> Bud Dodson
>
> > 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
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> Aron Broom M.Sc
> >> PhD Student
> >> Department of Chemistry
> >> University of Waterloo
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
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>
> --
> M. L. Dodson
> Business email: activesitedynamics-at-gmail-dot-com
> Personal email: mldodson-at-comcast-dot-net
> Gmail: mlesterdodson-at-gmail-dot-com
> Phone: eight_three_two-five_63-386_one
>
>
>
>
>
>
>
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Received on Sun Feb 26 2012 - 13:00:02 PST
