You can set the mdvel flag to print out velocities and check for yourself.
It will vibrate around its initial location. Don't forget that every single
atom is restrained with a harmonic potential already -- to any atom they're
bonded to and that is 2 bonds away, yet they still acquire velocities.
Also, if the restraints are weak enough, the coordinates will be able to
migrate a couple angstroms here and there (since they should be weaker than
a bond I'd say).
On Thu, Jun 24, 2010 at 12:52 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> But if we restraining the position then what will be the velocity of
> restraint
> atom when we heat?
> > 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
> >> >>
> >> >> _______________________________________________
> >> >> 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
> >> > _______________________________________________
> >> > 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
> > _______________________________________________
> > 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 - 22:30:03 PDT
