AMBER Archive (2009)

Subject: RE: [AMBER] Setting a constrain in one direction

Date: Fri Aug 28 2009 - 09:35:57 CDT

How are you defining which plane the atom is in? Restraints in AMBER tend
to be defined relative to other atoms. For example, it's possible to define
a plane of atoms (say, a nucleobase) and restrain the angle between the
normal of that plane and the vector from the center of mass of your plane to
the other atom. This will give you behavior something like you described:
to hold your atom in the plane of the plane of atoms, you'd set the
equilibrium angle to be 90 degrees. The restraint won't be truly harmonic
with respect to motion of your atom parallel to the normal of the plane --
instead, it's harmonic with respect to azimuthal motion. This is covered in
more detail in chapter 6 of the AMBER manual.

If you need to restrain the absolute coordinates of your atom rather than
restraining it relative to others, this is fairly tricky to do with AMBER's
restraints, short of adding a plane of atoms far from your system, fixing
their xyz position with ntr=1, and then using a restraint like the one
described above relative to that. That's not the most desirable solution,
obviously, but I'd look and see if you can accomplish your goal with a
relative restraint.

Matthew Seetin
University of Rochester Medical Center

-----Original Message-----
From: [] On Behalf
Of Darren Yang
Sent: Thursday, August 27, 2009 11:16 PM
Subject: [AMBER] Setting a constrain in one direction

Hi, Amber users.

I need help setting up a special type of MD simulation. Basically, I want to
have one atom in my system able to move in a plane (X/Y for example), and
have a harmonic potential constrain in the Z direction. I am not quite sure
how to do this or if there is a way?

Any suggestion will be greatly appreciated!
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