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From: M. L. Dodson <mldodson.comcast.net>

Date: Sun, 26 Feb 2012 07:46:51 -0600

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
*

*>> _______________________________________________
*

*>> AMBER mailing list
*

*>> AMBER.ambermd.org
*

*>> http://lists.ambermd.org/mailman/listinfo/amber
*

*>>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

Date: Sun, 26 Feb 2012 07:46:51 -0600

On Feb 26, 2012, at 12:05 AM, kirtana S wrote:

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

-- 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Feb 26 2012 - 06:00:03 PST

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