From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Sep 19 2017 - 12:23:46 CDT
NAMD follows the CHARMM convention for this. Although I'm not familiar
with the CHARMM internal code, they do report the formula without the 1/2
that Brian already pasted.
The Colvars manual specifies its harmonic formula explicitly to avoid
confusion, particularly because of the vague NAMD definition of the keyword.
On Tue, Sep 19, 2017 at 12:39 PM, Brian Radak <bradak_at_anl.gov> wrote:
> Yes - but that is *only in the memory optimized version*, which is barely
> used except for extremely large systems on large supercomputers.
> In the vast majority of instances, the force constant is just the value
> from the PDB file, usually stored as the B-factor. This is what is
> indicated by the manual.
> On 09/19/2017 12:33 PM, Victoria Lim wrote:
> 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
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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