Dear Romelia,
I am trying to reweight my aMD trajectory and need to know what values 3)
and 4) mean. Could you please explain how these factors are derived?
thanks in advance,
Thomas
On 8 October 2012 11:25, 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 Δt* in the accelerated MD
> > which one can find by using the equation Δt 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Sat Mar 02 2013 - 06:00:02 PST
