AMBER Archive (2001)

Subject: Re: lipid bilayer MD simulations

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Mar 06 2001 - 13:48:02 CST

        This is because the old prep way
        allowed you to specify the order of the three atoms

Meaning the 3 peripheral atoms. For a definition of improper
torsions, see http://www.amber.ucsf.edu/amber/newparams.html -

                                  J
                                  |
                                  K
                                 / \
                                I L

                           Improper I-J-K-L

I believe non-planar impropers are needed in the united-atom ff
because missing H's deprive the system of torsions that would
define the heavy-atom geometry.

Bill Ross