[gmx-users] EnMin & constraints: Hamletic doubt

Nicola Staffolani n.staffolani at unitus.it
Thu Jun 19 10:11:25 CEST 2014

Dear GMX community,

​I am running simulations of a solvated protein on a (frozen) Au substrate,
but I think that my question is so basic that it falls outside the details
of my case...

So, the question is: when I prepare the system by minimizing the energy,
should I set constraints = all_bonds, h_bonds or none?
IMHP, I should set it to all_bonds, otherwise I may risk that the system's
energy minimum corresponds to a configuration very different from the
initial one... However, I saw  somebody is using constraints = none and I
was wandering why...

Would somebody take the pleasure to embark on the discussion of such an
issue with me? Thnx in advance,

Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36

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