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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