[gmx-users] constraints and restraints

Grazia Daminelli Grazia.Daminelli-Widany at TU-Berlin.DE
Wed Feb 8 11:18:24 CET 2006

Hi everybody,

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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