can you tell us how you are actually doing it? for example, do you use
imin=5 in sander, or are you reading each frame as a separate sander/pmemd
run? we need to know the details in order to suggest improvements.
On Thu, Oct 17, 2019 at 9:35 AM 杨明俊 <mjyang.dicp.ac.cn> wrote:
> 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!
>
> Mingjun
>
>
> > -----Original Messages-----
> > From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
> > Sent Time: 2019-10-17 18:54:45 (Thursday)
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > 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 <mjyang.dicp.ac.cn> 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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> > >
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Received on Thu Oct 17 2019 - 11:00:03 PDT
