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

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Date: Mon, 30 Jan 2017 11:11:23 +0000

On Mon, 30 Jan 2017 10:22:04 +0000
Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk> wrote:

> 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?

I suggest to have look through the literature esp. the works by P.
H├╝nenberger, e.g. http://dx.doi.org/10.1063/1.4826261 .


> 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.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 30 2017 - 03:30:02 PST
Custom Search