[gmx-users] constrain h-bonds

[Nguyen Hoang Phuong]

On Wed, 11 Dec 2002, Anton Feenstra wrote:

> Nguyen Hoang Phuong wrote:
> > 
> > On Fri, 6 Dec 2002, K.A. Feenstra wrote:
> > 
> > > Nguyen Hoang Phuong wrote:
> > >  > Dear All,
> > >  >
> > >  > I would like to do simulation for the system consisting a peptide in
> > >  > flexible waters. I would like to constrain the h-bonds of the peptide but
> > >  > not for waters. Does anyone know how to do that? Thanks in advance.
> > >
> > > Are you sure you'd want to do that? It doesn't make sense to me...
> > 
> > yes, that's what I want to do. I want to constrain the hbonds of peptide
> > but not for hbonds of waters.
> 
> Wait, first let's sort out something. Do you mean hydrogen bonds,
> as in the interaction between a hydrogen bond donor (e.g. -OH group)
> and an acceptor (e.g. O=C group), or do you mean a covalent bond 
> with a hydrogen atom, as in the bond between O and H in an -OH group?
> 
> Both options are possible, but quite different obviously...

The covalent bonds (e.g N-H of peptide or O-H of waters). My peptide has
only one N-H bond and I would like to constrain this bond. If I set
constraint = hbonds in *mdp file then O-H bonds of waters are also
constrained but I don't want the semiflexible waters.

> 
> 
> -- 
> 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   |
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