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

Miguel Quiliano Meza rifaximina at gmail.com
Wed Apr 7 23:30:57 CEST 2010

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:

 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
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