[gmx-developers] Suggestion : annealing restraints
michel.cuendet at isb-sib.ch
Fri Aug 7 21:19:00 CEST 2009
Doing many independent simulations of the same system (with same
conformation but different 50K initial velocities), I noticed that most
of the variation between trajectories appears at the exact moment when
initial restraints on heavy atoms are released. This seems to be a
rather violent event for the system. Some people do several short
simulations with decreasing restraint strength before complete release.
In the charmm community for example, decreasing restraints step by step
is common practice, since this is easily automated in a charmm script.
The most gentle and most convenient way to release restraints would be
in a continuous fashion.
A nice feature in gromacs would be a set of keywords similar those of
the simulated annealing function, except that it would scale the
restraint harmonic constants instead of temperature. This way, the user
could, in a single run, heat up the system with restraints, let it
equilibrate, and then progressively remove the restraints. One could
even imagine a group-based scaling, with groups defined with a
restr_grps keyword for example.
If the usefulness of such a feature is recongnized, this should be easzy
Michel Cuendet, Ph.D
Molecular Modelling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
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