XY constraints with center of mass movements

From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Mon Dec 09 2013 - 11:29:12 CST

Hi all,

I am doing an SMD simulation where I am pulling a molecule in Z-axis for
about 40 Ang (through the lipid bilayer from slightly above the head
groups). During my simulation I have seen the molcule moving too much in X
and Y direction too (it even fluctuating between the PBC copies). I have
tried then constraining it using selective constraints using selectConstrX
and selectConstrY options in harmonic constraints option. In this case the
molecule went straight down in Z-axis not moving (rotating) in its axis.

I would like to pull the molecule in Z direction with its center of mass
movements. I need your help.


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