[gmx-users] constrain h-bonds

[Nguyen Hoang Phuong]

thank Anton. It works.


> the N-H bond in your peptide to a constraint. This is very simple.
> If your N is atom 5 in your peptide, and the H is atom 6, you will
> have this in your .top file:
> 
> [ bonds ]
>      5      6     1
> 
> Possibly, there are parameters on the line, like
> [ bonds ]
>      5      6     1      0.105     4e6
> 
> (I just made up the numbers, don't blame me if they are nonsens).
> 
> You should comment out this one line (put a ';' in front) and make
> a [ constraints ] section with these atoms, and the distance, like:
> 
> [ constraints ]
>      5      6     1      0.105
> 
> Be sure you take the right distance! 
> Put the [constraints] in front or just after the [bonds].
> 
> 
> -- 
> Groetjes,
> 
> Anton
>  ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "Hmm, It *Does* Go Well With the Chicken" (Beastie Boys)  |
> |________|___________________________________________________________|
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