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/
> >> (801) 587-9652
> >> (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 - 11:00:02 PDT
