Re: [AMBER] Constraints

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 15 Nov 2016 14:20:07 -0500

As mentioned, you can use restraints to approximate constraints, although
this will formally introduce some impact on any computed thermodynamic
properties. Also, the stronger your restraints are, the shorter you have
to make your timestep (the opposite of what you'd see if you actually used
true constraints).

Rigid body dynamics (excluding for <=3 atom molecules like water) is not an
easy problem. There is a script/input file for OpenMM that will implement
rigid body dynamics by treating all atoms as "virtual sites", I believe.
See
https://simtk.org/plugins/moinmoin/openmm/VirtualRepository#OpenMM_Code_Repository
(under "Rigid Bodies").

If restraints are good enough, then you can do that in a straightforward
way with Amber.

HTH,
Jason

On Tue, Nov 15, 2016 at 9:21 AM, Roitberg,Adrian E <roitberg.ufl.edu> wrote:

> Not easy, but could set nmropt=1 and create a boatload of restraints with
> large force constants, for every bond, angle and torsion in your molecule.
>
> You can also restrain all pair distances.
> ‚Äč
>


> If you a willing to live with small internal movements of your molecule,
> you can restrain the distances between 6 atoms far apart, creating
> something like axes of inertia.
>
> Trial and error will be needed for this.
>
>
>
> Sent from my Verizon, Samsung Galaxy smartphone
>
>
> -------- Original message --------
> From: David A Case <david.case.rutgers.edu>
> Date: 11/15/16 6:19 AM (GMT-07:00)
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Constraints
>
> On Fri, Nov 11, 2016, Ol Sta wrote:
> >
> > I have a question regarding molecular constraints.
> > What is the easiest way of constraining a molecule
> > in a box of water solvent ?
> >
> > I would like to constrain all bonds, bends, and torsions,
> > keeping the geometry fixed but let the molecule float
> > around in the box.
>
> Amber does not offer any easy way to do this sort of calculation.
> Generally,
> Amber users would be likely to use restraints (setting ntr=1), and let the
> water equilibrate around the solute. But we don't have any good way that I
> know of to do rigid body dynamics. (I hope someone will chime in if I am
> missing something here....)
>
> ...dac
>
>
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-- 
Jason M. Swails
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Received on Tue Nov 15 2016 - 11:30:02 PST
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