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,
Stefan
________________________________________
From: Hannes Loeffler [Hannes.Loeffler.stfc.ac.uk]
Sent: Monday, January 30, 2017 9:02 AM
To: amber.ambermd.org
Subject: Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd
On Sun, 29 Jan 2017 15:07:13 +0000
Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk> 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?
Cheers,
Hannes.
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Received on Mon Jan 30 2017 - 02:30:02 PST
