From: Brian Radak (bradak_at_anl.gov)
Date: Tue Sep 19 2017 - 11:39:05 CDT
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
> On Tue, Sep 19, 2017 at 6:30 AM, Brian Radak <bradak_at_anl.gov
> <mailto: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 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,
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643 <tel:%28630%29%20252-8643>
> brian.radak_at_anl.gov <mailto:brian.radak_at_anl.gov>
-- 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
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