Re: [AMBER] About position restrains

From: Thomas Cheatham <>
Date: Wed, 22 Nov 2017 15:22:09 -0700 (MST)

> I am having a question regarding how the position restraint potential is
> calculated. As I understand, it is an harmonic potential as described in
> the manual, which exponentially increases as does the RMSD to reference
> structure. My question is if that RMSD is mass weighted (as seem to be
> most default settings for RMS calculations in amber) or just plain RMSD.

There are multiple types of restraints in AMBER, including RMSD restraints
(see the section 20.4 on targeted MD in the latest manual), however
Cartesian restraints or harmonic positional restraints are not RMSD
restraints and are not explicitly mass weighted (although their influence
will be effected by the mass and force constant chosen). There is a fixed
force constant per atom selection (restraint_mask) and each atom is
restrained to the initial coordinates specified in the supplied refc file.


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Received on Wed Nov 22 2017 - 14:30:02 PST
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