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 42=2 while it is 41=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 146270216  Ph.:(585) 275 67 66 (Office) 
 http://www.pas.rochester.edu/~yildirim/ 


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