It sounds to me like you just want to use the regular "NMR-style"
restraint system. A simple harmonic distance restraint between two
groups of atoms is what you want, I believe, based on your description.
This method does not "fix" one group, it only operates on the distance
between them, but I think it fits what you want to do.
Read section 6 of the Amber11 manual, and in particular, study
section 6.1.
If you really do need to fix one group of atoms, then calculate
the PMF of another group approaching them, I know of no way to do
this with Amber. Some one speak up if there is a way I don't know
about. Maybe the belly feature will do this? Is belly even still
in Amber?
Good luck,
Bud Dodson
On Feb 26, 2012, at 2:46 PM, kirtana S wrote:
> 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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>>
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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 - 14:30:02 PST
