[AMBER] steered md at constant force

From: Batuhan Kav <bkav13.ku.edu.tr>
Date: Wed, 9 Jan 2019 12:00:56 +0100

Dear All,

Our system is composed of a lipid bilayer with a single anchored
glycolipid. We would like to apply a constant force to the center of
mass of the glycolipid along with the membrane normal (which will be
z-axis) to study the displacement of certain atoms in the glycolipid as
a response to this constant force. From an earlier question at the mail
list (http://archive.ambermd.org/201104/0662.html), I see that a
constant force SMD can be achieved with defining the distance restraints
(in Amber10), however it seems like the distance restraints are applied
to certain singular atoms. In this regard, I have three questions:

1) Can I apply restraints on center of mass of a certain group of atoms?

2) How can I set the applied force to act along only one axis (z-axis)?

3) Is there a way to specify/set the magnitude of the force to a
constant value?

As the last correspondence in the mail list I found is dated 8 years
old, I wanted to ask these questions in case the procedure has changed.



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Received on Wed Jan 09 2019 - 03:30:03 PST
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