[gmx-users] constrain h-bonds

[Anton Feenstra]

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'.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
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