From: Brian Radak (bradak_at_anl.gov)
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.
HTH,
Brian
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 brian.radak_at_anl.gov
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:36 CST