Re: [AMBER] parallel constraints SMD

From: Jason Swails <>
Date: Fri, 24 Aug 2012 11:51:19 -0400

On Fri, Aug 24, 2012 at 11:39 AM, e g <> wrote:

> Hello,
> I would like to run a steered-MD calculation with amber, using several
> distance constraints simultaneously (i.e. steered to decrease several
> different distances at the same time). Is this possible? Or can there only
> be 1 steered distance? When I attempt to submit such a run with the
> below-listed input files, either the 1st constraint is accepted, and the
> rest are ignored, or I get the following error:
> ----------
> "application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0"
> "In Jarzynsky runs, there must only one restrain, stopping program"

This would suggest only one restraint is allowed (which is confirmed in
tests that I've recently seen).

What I would suggest doing is setting up a steered MD simulation whose
reaction coordinate is not a simple distance, but rather a linear
combination of multiple distances. For instance, for a proton shuttle
between two atoms, you may make the reaction coordinate the difference
between two distances (the distance between the H and the atom it's
transferring TO minus the distance between the the H and the atom it's
transferring FROM).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Fri Aug 24 2012 - 09:00:04 PDT
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