Re: [AMBER] restraints in simulations

From: Jason Swails <>
Date: Tue, 26 Jan 2016 07:50:18 -0500

On Mon, Jan 25, 2016 at 1:23 PM, Lara rajam <> wrote:

> Dear Amber
> I would like to bring the ligand from far distance from the receptor to the
> surface of the receptor. The atoms that I have selected on the ligand and
> on the receptors are now 22.5 angstrom apart. I need to pull the ligand to
> near the surface of the receptor, which is 16.2 angstrom from the receptor
> fixed atom. I have used the following parameters to run the simulation. I
> have enclosed restrain file too. In restrain for these kind of simulation
> the ifvari=1 should be applied. When I see the distance change between the
> two points it is not linear it jumps randomly. How I can control the
> variables to make the force so that the distance decrease with respect to
> time is linear.

‚ÄčIt sounds like you are trying to do "steered" molecular dynamics. You can
find an example of a steered MD simulation in $AMBERHOME/test/jar. I would
also recommend reviewing some literature to see how this type of study has
been performed in the past (in my experience, two species are usually
pulled *apart* rather than *together* due to the decrease in entropy
associated with binding events.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 26 2016 - 05:00:03 PST
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