I think the information you're looking for is in this paper:
Accelerated molecular dynamics: A promising and efficient simulation method
for biomolecules
Hamelberg, Donald; Mongan, John; McCammon, J. Andrew
J. Chem. Phys. 120, 11919 (2004); doi: 10.1063/1.1755656
-Christina
On Wed, May 28, 2014 at 11:37 AM, James Starlight <jmsstarlight.gmail.com>wrote:
> Thanks for suggestions Dan!
>
> Could you tell me how the increasing of alpha parameter (Which will affect
> on the smoothness of the potential energy landscape) instead of increasing
> of boost could influence on reweighing?
>
> James
>
>
> 2014-05-28 17:57 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
> > On Wed, May 28, 2014 at 1:18 AM, James Starlight <jmsstarlight.gmail.com
> >
> > wrote:
> > > 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 ?
> >
> > This is really a question that can only be answered through research.
> > What boost parameters are "reasonable" depends on what you want to
> > see. Keep in mind that recovering equilibrium properties by
> > reweighting via boost energies becomes less accurate as your boost
> > energy increases. You can reweight based on population, but I'm not
> > sure how that is affected by system size/boost energy magnitude. See
> > Markwick & McCammon, PCCP, 2011, 13, 20053-20065 and Sinko et al.,
> > JCPB, 2013, 117, 12759-12768 for more on aMD reweighting.
> >
> > If you're not seeing the affect you want on a given timescale you can
> > adjust the boost parameters, but you may increase the overall noise in
> > your system. Alternatively, you could run a H-REMD simulation with
> > your lowest replica having no boost and the remaining replicas having
> > increasing amounts of boost, which implicitly takes care of the
> > reweighting for you (though you will probably have to play around with
> > the replica boost values to get reasonable exchange acceptance rates);
> > we have recently done this for an RNA tetranucleotide system (Roe et
> > al., JCPB, 2014, 118, 3543-3552).
> >
> > If you haven't already, it is probably worthwhile to do a conventional
> > MD simulation so you have some sort of baseline to compare to.
> >
> > -Dan
> >
> > >
> > > 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/
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> > >> (801) 585-6208 (Fax)
> > >>
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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 - 12:00:03 PDT
