Re: [AMBER] Estimating time in AMD

From: Soumya Lipsa Rath <soumyalipsabt.gmail.com>
Date: Mon, 8 Oct 2012 15:01:46 +0530

Thanks Romelia for the reply

I was searching an answer for e^V[r(t*i*)], but the amd.log file gives us
information about the scaling and V of total and dihedral boot potential
only. I wanted to calculate the accelerated time step to get an estimation
of the real time.

Thanks,

Soumya

On Mon, Oct 8, 2012 at 1:55 PM, Romelia Salomon <romelia.caltech.edu> wrote:

> Dear Soumya
>
> The amd.log file contains the AMD pertinent information produced along the
> calculation. It is printed every time the trajectory is printed, as those
> are the configuration points that will be available for analysis.
>
> The information being printed is:
>
> 1) The total potential energy for that step (without the extra added by
> AMD, to keep in reference with mdout)
> 2) the total dihedral energy for that step (without the extra added by
> AMD, to keep in reference with mdout)
> 3) factor by which total forces are scaled
> 4) factor by which dihedral forces are scaled
> 5) energy added by AMD to the total potential energy
> 6) energy added by AMD to the dihedral energies
>
> I hope this helps.
>
> Romelia
>
>
> > Dear Amber Users,
> >
> > I wanted to calculate the modified time step t* in the accelerated MD
> > which one can find by using the equation t x boost factor. How can one
> > get
> > the value for boost factor?
> >
> > Thanks
> >
> > Soumya
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> ****************************************
> Romelia Salomon
> Walker Group
> 398 San Diego Supercomputing Center
> UC San Diego
>
>
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>
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Received on Mon Oct 08 2012 - 03:00:03 PDT
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