From: Victoria Lim (limvt_at_uci.edu)
Date: Tue Sep 19 2017 - 11:33:46 CDT
I looked through a few versions of the user guide (such as
http://www.ks.uiuc.edu/Research/namd/2.11/ug/node27.html) but did not see
the particular formula used.
Thanks for looking through the code Brian! Out of curiosity, when you say
the force constants are read as simple Boolean flags, do you mean that if k
is zero, the Boolean variable goes to false, and the atom is unrestrained?
On Tue, Sep 19, 2017 at 6:30 AM, Brian Radak <bradak_at_anl.gov> wrote:
> 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
> 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,
> 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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