[gmx-users] constraints and restraints
Grazia.Daminelli-Widany at TU-Berlin.DE
Wed Feb 8 11:18:24 CET 2006
I have some basic questions about constraining and restraining procedures.
Constraints are conditions that the system is forced to satisfy and
restraints are penalties set to encourage a particular value, is that
1) can I apply constraints without restraints (or restraints without
constraints)? which advantages do I have if I apply both simultaneously
(as it is in the Gromacs tutorial)?
2) if I have a protein in water, is it possible to constrain only a
part of the system (only protein, only bb)? as far as I know the mdp
option *constraints= all-bonds* will constrained indeed all bonds,
even those of water if I am using a flexible model, isn't it?
3) if I apply constraints and I am using rigid water molecules, the
SETTLE algorithm will apply only to water molecules and LINCS/SHAKE
algorithms will apply to rest of the system, is that correct?
Thanks in advance for comments and explanations.
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