Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option?

From: Brian Radak (
Date: Tue Sep 19 2017 - 08:30:20 CDT

This a worthwhile question - is this not in the user guide? I would
regard that as an oversight.

Looking at the code, the energy is computed as:

E = k(r - r_ref)**n

where n is the (positive integer) exponent and defaults to 2.

Something I did not now, but is probably of little consequence, is that
the memory optimized version of NAMD appears to ignore the force
constants in the reference file and instead reads them as simple boolean
flags. Otherwise k is computed as the value in the given PDB column
times constraintScaling.



On 09/19/2017 02:37 AM, Victoria Lim wrote:
> Dear NAMD users,
> Do the harmonic restraint parameters specified by the "constraints"
> option contain the factor of one half in the harmonic potential? I
> realize the "extraBonds" option does /not/ contain this factor,
> whereas the harmonic potential in the colvars module does have the
> 1/2. However, I could not find an explicit formula for the constraints
> option.
> Thank you,
> Ria

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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