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

From: Carlos Simmerling <>
Date: Thu, 17 Oct 2019 06:54:45 -0400

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
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Received on Thu Oct 17 2019 - 04:00:01 PDT
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