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

From: Stefan Ivanov <>
Date: Mon, 30 Jan 2017 10:22:04 +0000

Hi Hannes,

Once again, thank you very much for your reply and help.

Yes, I am aware the end states have different charges. Does this warrant any changes to my input parameters/special consideration?

Kind regards,

From: Hannes Loeffler []
Sent: Monday, January 30, 2017 9:02 AM
Subject: Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd

On Sun, 29 Jan 2017 15:07:13 +0000
Stefan Ivanov <> wrote:

> Hi Hannes, hello all,
> The trajectories seem to be running fine now, but at lambda = 1,
> during the first few thousand steps of heating, the MBAR energies for
> 0.0 skyrocket:

Yes, this shows up in cases when large parts of a molecule are
disappearing or appearing, so in your case from either end-state
extrapolating to the other. This is also happening in absolute
transformations at low lambdas. I guess this is a feature of the
softcore function in use.

BTW, are you aware that you have different charges (+1 vs +2) at the
end states?


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