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.
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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Received on Tue Nov 15 2016 - 06:30:03 PST
