AMBER Archive (2006)

Subject: Re: AMBER: Qestion about input for RESP program

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed May 24 2006 - 23:49:11 CDT

They are not the same thing. Think about the following
example:

Let's say that I am constraining in the following way:

 === 1st way ===
      2 0.0
      1 1 1 2
      2 0.0
      1 3 1 4
 ================

Let's say the meaning of 1,2,3,4 is the following:

1 = a
2 = b
3 = c
4 = d

Then
   a+b = 0
and
   c+d = 0

This is the constrains that we have in this 1st Method.

Let's say that the 2nd Method is the following:

 === 2nd way ===
      4 0.0
      1 1 1 2 1 3 1 4
 ===============

In this case, the constraint is;

a+b+c+d=0

So, let's analyse it:

1st Method:
  If a=2 and c=2 => b=-2 and d=-2

2nd Method:
  If a=2 and c=2 => b+d=-4
=> If b=1 => d=-5
or
   If b=2 => d=-7
or
   If b=-2 => d==2
...

As you can see, the 2nd method has more possibilities than the 1st method.
The reason is because of the degrees of freedom differences. The
definition of degrees of freedom is;

Number of unknowns - number of unique equations = dof

The degrees of freedom (dof) of the 1st method is 4-2=2 while it is 4-1=3
in the 2nd method.

The meaning is; if you define 2 unknown variables in the 1st method, u
can solve the equations, where if you define 3 unknown variables in the
2nd method, u will solve the equation.

Hope this helps. Best,

On Wed, 24 May 2006, JunJun Liu wrote:

> Dear All,
>
> On the page 235 of Amber8 manual, it states that 7.1th "area" is the list
> of atoms that need constraints. Now, I have a question, this constraint
> list can be written in the following two ways:
> === 1st way ===
> 6 0.0
> 1 1 1 2 1 3 1 4 1 5 1 6
> 6 0.0
> 1 17 1 18 1 19 1 20 1 21 1 22
> ================
>
>
> === 2nd way ===
> 12 0.0
> 1 1 1 2 1 3 1 4 1 5 1 6
> 1 17 1 18 1 19 1 20 1 21 1 22
> ===============
>
> These two ways of defining the list of charge constrained atoms are the
> same to me. But the results are different. Can anybody tell me why there's
> such a difference? I checked the source code and found it's related the
> 'nlgrng" varible. What's the role of this varible?
>
> Thanks!
>
> Liu
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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