Dan,
I've noticed that 3.6 kcal/mol is very small boost applied to all residues
of my protein (400 a.a). Takng into account that this boost value have
been saved in log after first 5000 timesteps of aMD but <DIHE> was
reasonable big in comparison to cMD how I could make suggestions about
reasonability of applied boost values ?
James
2014-05-27 17:39 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> On Sun, May 25, 2014 at 7:28 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> >
> > EAMD_BOOST = 3.6823
> >
> > does this value corresponded to the added dihedral term of all my system
> or
> > to one degree of freedom residue ?
>
> This is the total AMD boost applied to all dihedrals.
>
> -Dan
>
> >
> > Also I'll be thankful if you provide me with some script suitable for
> > calculation of averages of all output values like dihedral energy etc
> >
> >
> > TFH,
> >
> > James
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Wed May 28 2014 - 00:30:02 PDT
