Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd

From: Stefan Ivanov <>
Date: Mon, 30 Jan 2017 14:20:43 +0000

I've suspected a bug's lurking somewhere in the code ever since these problems started. After minimization the coordinates are fine, though. It's during or after heating that the problems start. Do you have any advice how I could get around these problems? So far I've been playing around with the duration of the heating and the equilibration and the strength of the restraints. Simulating the ligands in isolation with restraints of 99 kcal/mol*A^2 worked till around 60 ps after which they became distorted. Reducing the restraints to 10 didn't produce any distortions but the equilibration step couldn't start:

     Error : Atom 1 does not have match in V1 !

Maybe if I shorten heating and equilibration to 10 ps each, I can get it to work.

Worst case scenario is I run production MD straight after minimization, maybe for an extra 200 ps and discard the first 200 ps while the temperature and density adjust.

I just don't know what else to do.

Again, your advice is more than welcome.

Best wishes,


From: Hannes Loeffler []
Sent: Monday, January 30, 2017 1:56 PM
To: Stefan Ivanov
Subject: Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd

On Mon, 30 Jan 2017 12:35:01 +0000
Stefan Ivanov <> wrote:

> Yesterday you mentioned that identical atoms move identically, so how
> could these misalignment errors be ocurring?

A bug in pmemd that doesn't synchronise coordinates after minimisation.

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Received on Mon Jan 30 2017 - 06:30:03 PST
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