[gmx-users] constrain h-bonds

[Nguyen Hoang Phuong]

On Wed, 11 Dec 2002, Anton Feenstra wrote:

> Nguyen Hoang Phuong wrote:
> > 
> > The covalent bonds (e.g N-H of peptide or O-H of waters).
> 
> OK - that was my initial guess also.
> 
> > 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.
> 
> No - default spc water uses 'settle' to constrain bond lengths and angles.
> Setting 'constraint = hbonds' or not in .mdp will not change that.
> You can look in the file spc.itp, where the 'settle' is defined explicitly.
> Try running grompp with the 'constraint = ' option set first to
> 'none' and then to 'h-bonds', and compare the two .tpr files with
> 'gmxchech -s1 none.tpr -s2 hbonds.tpr'. That will tell you exactly
> which interactions have changed. You should only see the disappearance
> of one bond and the appearance of one 'shake' or 'constraint'.

but what happen if I use the option -DFLEX_SPC? Will the O-H bonds of
waters be constrained if the option constraint = hbonds is defined?

> 
> 
> -- 
> 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)  |
> |________|___________________________________________________________|
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
>