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
Received on Wed Jun 23 2010 - 22:00:03 PDT
