rigid body model

From: Hidekazu WATANABE (evergreen_tow_at_yahoo.co.jp)
Date: Fri Feb 08 2008 - 02:24:30 CST

Hi, everyone.

I have a question of rigid body model.

I'd like to apply the rigid body model for a molecule,
but to allow the rotation and the translation of the molecule.

For example, I want to constrain the molecule with resID 1,
the following commands are typed in VMD console at first;
========
set all [atomselect top all]
set fix [atomselect top "resid 1"]
$all set beta 0
$fix set beta 1
$all writepdb kotei.pdb
========.

And then, the description of the configuration file is as follows,
but the molecule with resID 1 is NOT constrained at all.
========
constraints on
consRef kotei.pdb
consKFile kotei.pdb
consKCol B
========

If the description of the configuration file is as follows,
the molecule with resID 1 is fixed in the space.
However, rotation and translation are also frozen.
========
fixedAtoms on
fixedAtomsFile kotei.pdb
fixedAtomsCol B
========

Would you show me how to treat the rigid body allowing
the rotation and the translation?

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