On Wed, Jun 23, 2010 at 12:49 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Then why during heating and equilibration why not during production run?
>
Because it's not a huge perturbation, and imposing restraints adds the
assumption that the coordinates will not appreciably change.
>
> And during heating at one side we are heating the ststem and another we
> restraint i. e. we are heating the stem as well as restraing its velosity
> will
> it not affect the system energy or conformation very much?
>
We are not restraining the velocities, we are restraining the positions.
The velocities will still scale up such that the total temperature reaches
the target. What this process does is allow the protein to settle into a
comfortable conformation that will not blow up when charges are changed.
Then we let it evolve as it wants to without restraints.
>
> > Instabilities are more likely due to the way constant pH works. Charges
> on
> > titratable residues abruptly change when a protonation change is
> accepted,
> > which can exacerbate a slightly unfavorable structure.
> >
> > On Wed, Jun 23, 2010 at 10:39 AM, Sangita Kachhap <sangita.imtech.res.in
> >wrote:
> >
> >>
> >> Hello all
> >>
> >> Why restraint is used during heating process in case of constant pH
> >> simulation?
> >>
> >> With regard
> >> Sangita Kachhap
> >> JRF
> >> BIC,IMTECH
> >> CHANDIGARH
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
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> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jun 23 2010 - 11:00:04 PDT
