Re: [AMBER] more efficient TI rerun over existing trajectory

From: 杨明俊 <>
Date: Thu, 17 Oct 2019 21:35:27 +0800 (GMT+08:00)

Hi Carlos,

   Thanks for your response. What I am working on is trying to improve the production of hydration free energy by adjusting atomic charges and vdw parameters. To this end, I firstly run the simulation with the original Hamiltonian, e.g. H0. Then I changed the selected atomic charges or vdw parameters, resulting in a new Hamiltonian, e.g. H1. I'd like to know if the adjustment of charge or vdw parameters can produce better predicted HFE against experimental measurements. To reduce the computational cost, I used reweighting method to get the HFE under H1 over the trajectory (T0) generated with H0. Thus I need to rerun the energy calculations using H1 over T0. The problem is when too many frames are recorded in T0, it will take too much time to finish the rerun, especially when MBAR or WHAM is used (which requires Nframe x Nstate x Nstate energy calculations). Thus I'd like to know if there is a way to do the energy rerun more efficiently with TI.

Thanks for any suggestions and comments!


> -----Original Messages-----
> From: "Carlos Simmerling" <>
> Sent Time: 2019-10-17 18:54:45 (Thursday)
> To: "AMBER Mailing List" <>
> Cc:
> Subject: Re: [AMBER] more efficient TI rerun over existing trajectory
> Can you tell us exactly what you are doing, so we can see if it might be
> improved? Also what do you mean by "very painful" - which aspect
> specifically would you like to improve?
> On Wed, Oct 16, 2019, 11:25 PM 杨明俊 <> wrote:
> > Dear Everyone,
> >
> >
> > I am studying a reweighting scheme with TI for relative hydration free
> > energy calculation, for which I need to rerun the trajectory with a
> > modified Hamiltonian. However, I haven't figured out an efficient way to
> > rerun the trajectory. Currently, I firstly extract individual frames from
> > the trajectory and then recompute the energy for this frame with different
> > Hamiltonian. However, this is very painful when there are too many frames
> > included in the trajectory. Does anyone know a way to do the rerun with TI
> > over existing trajectory more efficiently?
> >
> >
> > Thanks in advance!
> >
> >
> > Mingjun
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
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Received on Thu Oct 17 2019 - 07:00:02 PDT
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