[gmx-users] an energy minimization question, working with H-BONDS

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 7 23:39:17 CEST 2010

Miguel Quiliano Meza wrote:
> Dear Users.
> I am a relative new user of GROMACS and I have some doubts:
> I would like to perform a energy minimization (with water and iones) of 
> a crystal in orden to re-build the H-bonds responsible of the secundary 
> structure, to achieve this goal I want to restraint the movement of the 
> protein (aminoacids) and permit the movement of the H-bonds as a 
> product of add Hydrogens with pdb2gmx.
> I think that this task could be define/establish in CONSTRAINS in 
> the ".mdp" file, I searched in the web and only find this:

First, understand that a "constraint" and a "restraint" are very different 
concepts in Gromacs:


Thus, the "constraints" keyword is unrelated to what you're looking to do.

Simple energy minimization will seek to relax the structure, forming favorable 
contacts and resolving large forces.  Whether or not this bears any useful 
information about the stability of secondary structure is debatable.  Running 
true MD is a better tool for that purpose, but EM should suffice to form any 
hydrogen bonds that are reasonably close in space.

I don't think it will be meaningful at all to restrain part of the protein and 
hope that hydrogen bonds in the backbone re-orient.  You'd essentially be fixing 
the side chain positions, which will not allow for much re-organization, not 
that I'd expect to see major changes during EM, anyway.


>       Bonds
>         constraints:
>     *none*
>         No constraints except for those defined explicitly in the
>         topology, i.e. bonds are represented by a harmonic (or other)
>         potential or a Morse potential (depending on the setting of
>         *morse*) and angles by a harmonic (or other) potential. 
>     *hbonds*
>         Convert the bonds with H-atoms to constraints. 
>     *all-bonds*
>         Convert all bonds to constraints. 
>     *h-angles*
>         Convert all bonds and additionally the angles that involve
>         H-atoms to bond-constraints. 
>     *all-angles*
>         Convert all bonds and angles to bond-constraints. 
> What option shoud I use for my objective? My objetive, is it possible to 
> do? I would be very grateful if someone can help me with some ideas or 
> advices.
> thanks in advance
> Miguel


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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