A problem with overly strong restraints is that the frequency of the
vibration increases, necessitating a smaller time step to keep the
simulation stable. Values of 10-100 should be quite adequate for
equilibration.
On Dec 14, 2017 5:25 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
> If you want utter rigidity, belly might be appropriate, though I believe
> it is unpopular among the better-educated, and I am not expert on the
> physics, so hopefully someone else will comment. In principle, it might
> be the better approximation to the artificiality of whatever method you
> are relating it to.
>
>
> On 12/14/17 2:18 AM, Leena Aggarwal wrote:
> > I want to keep the solute molecule restraint as I want to relate it with
> > theory results in which solute molecule is rigid.
> >
> > On Thu, Dec 14, 2017 at 3:45 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> It sounds like sitting in the car in the parking lot with the seatbelt
> >> on while the family goes in to Disney Land, but it shouldn't be what
> >> makes your taxes go up.
> >>
> >> Is there some reason you want to keep things rigid in that region?
> >>
> >>
> >> On 12/14/17 1:57 AM, Leena Aggarwal wrote:
> >>> Dear Amber Users
> >>>
> >>> How to decide the restraint_wt?
> >>>
> >>> I have tried with different restraint_wt values. More restraint_wt
> means
> >>> more tightly restrained. RMSD of the restrained coordinates becomes
> more
> >>> close to 0 as restraint_wt increases. In my system restraint_wt=9500
> >> gives
> >>> RMSD more close to zero.
> >>> Is there any disadvantage of taking so large value of restraint_wt.
> >>>
> >>>
> >>> Thanks
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Received on Thu Dec 14 2017 - 04:00:02 PST
