[gmx-users] constrain h-bonds

[Anton Feenstra]

Nguyen Hoang Phuong wrote:
> 
> 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?

Yes - in flexspc.itp normal bonds (O-H) and one angle (H-O-H) are
defined. Setting constrants = h-bonds will convert the bonds to
constraints. The angle will remain flexible.

So - if you want constraints on your peptide N-H covalent bond, and
you want flexible water molecules, you will need to *manually* convert 
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 |
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