[gmx-users] constraints and restraints

[Yang Ye]

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Grazia Daminelli
> Sent: Wednesday, February 08, 2006 6:18 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] constraints and restraints
> 
> 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
> correct?
> Then:
> 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)?
Yes. You can apply do so but it largely depend what you want to do...
> 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?
For water model which has section [ constraints ], there will be constraints
applied to them; with [ settle ], SETTLE will be applied.
> 
> 
> Thanks in advance for comments and explanations.
> 
> Grazia
> 
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