AMBER Archive (2004)

Subject: AMBER: free energy profile calculation

From: Martina Roeselova (
Date: Wed Jan 14 2004 - 15:14:48 CST


I am looking at interactions of small gas phase molecules with the
surface of various liquids (water and solutions of different salts). To
simulate the vacuum/liquid interface, I use a slab geometry employing
periodic boundary conditions, and I NEED to use Ewald for my systems. I
use SHAKE to freeze the intramolecular degrees of freedom in both the
water molecules as well as my gas phase molecule.

I would like to calculate the Gibbs free energy profile for a gas phase
molecule approaching the liquid surface along the normal to the
vacuum/liquid interface (z-axis).

vacuum |




I want to perform a series of runs in which I constrain ONLY the
z-coordinate of the CENTER OF MASS of my gas phase molecule within
certain window along the z-axis, allowing the gas phase molecule to move
in the x-y plane as well as rotate freely during each run (the
intramolecular vibrations of the molecule frozen using SHAKE). Is there
a possibility in AMBER to constrain the center of mass of a selected
group of atoms in such a way? Can someone teach me how to do it?

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to