[gmx-users] Using position restraiuts to "drive" a system into a paritcular state ?

Marc Baaden baaden at smplinux.de
Mon Nov 26 21:16:10 CET 2001


I have some questions about position restraints. Most of the time people
probably use them to restrain their system or parts of it to the initial
position while equilibrating other parts of the system.

What I would like to do is to start from a protein which is present in
one local minimum and use position restraints that refer to another state
also supposed to be a local minimum.

I would then (for the moment) simply like to perform an energy minimization
and see how the system is driven from its original state to the imposed one.

My problem is that - as far as I could investigate - the reference position
taken for the position restraints is the same as the starting structure.

So the question:
is there a way to use position restraints with respect to one structure/
conformation, but start the energy minimization (or later on MD) from
another structure ?

NB: In principle I could use distance restraints and either convert
    the absolute cartesian distances I have in a distance matrix, or
    use a dummy reference atom. But I wish not to pursue this path.

Thanks in advance,

  Marc Baaden

 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
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