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From: Ilyas Yildirim <yildirim.pas.rochester.edu>

Date: Thu, 25 May 2006 00:49:11 -0400 (EDT)

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
*

*>
*

*>
*

Date: Thu, 25 May 2006 00:49:11 -0400 (EDT)

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:

-- 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/ - --------------------------------------------------------------- ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Fri May 26 2006 - 21:05:20 PDT

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