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

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Sep 19 2017 - 13:03:04 CDT

> With an exponent that may be different from 2, the factor 0.5 becomes
rather arbitrary

It is. Then a factor of 1/n for any exponent n would have made sense, and
still followed the usual convention for n = 2. But we can't remake history,
can we?

Best,
Jerome

On 19 September 2017 at 19:29, Lennart Nilsson <Lennart.Nilsson_at_ki.se>
wrote:

> With an exponent that may be different from 2, the factor 0.5 becomes
> rather arbitrary, which is why we (CHARMM) dropped it.
>
>
>
> Best wishes,
>
> Lennart Nilsson
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Giacomo Fiorin
> *Sent:* den 19 september 2017 19:24
> *To:* NAMD list <namd-l_at_ks.uiuc.edu>; Brian Radak <bradak_at_anl.gov>
> *Cc:* Victoria Lim <limvt_at_uci.edu>
> *Subject:* Re: namd-l: What is the exact form of the harmonic potential
> used by the NAMD "constraints" option?
>
>
>
> 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.
>
>
>
> Giacomo
>
>
>
> 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
> 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
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3D9700-2BSouth-2BCass-2BAvenue-2C-2BBldg.-2B240-26entry-3Dgmail-26source-3Dg&d=DwMGaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=LHUFRvVwJemLmFw0kCqJX1ySoP2sxe1NAz1P0aO56x8&s=kvSaIV8vpc-ivAW0xng1KJJQw9MLUpidjnIzkiPRXlk&e=>
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
>
>
>
>
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3D9700-2BSouth-2BCass-2BAvenue-2C-2BBldg.-2B240-26entry-3Dgmail-26source-3Dg&d=DwMGaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=LHUFRvVwJemLmFw0kCqJX1ySoP2sxe1NAz1P0aO56x8&s=kvSaIV8vpc-ivAW0xng1KJJQw9MLUpidjnIzkiPRXlk&e=>
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
>
>
>
>
> --
>
> Giacomo Fiorin
>
> Associate Professor of Research, Temple University, Philadelphia, PA
>
> Contractor, National Institutes of Health, Bethesda, MD
>
> http://goo.gl/Q3TBQU
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_Q3TBQU&d=DwMGaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=LHUFRvVwJemLmFw0kCqJX1ySoP2sxe1NAz1P0aO56x8&s=32tfFAFKEiN2w4PcEabVSIWU-eZzyUqAMThrYHWTw5M&e=>
> https://github.com/giacomofiorin
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_giacomofiorin&d=DwMGaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=LHUFRvVwJemLmFw0kCqJX1ySoP2sxe1NAz1P0aO56x8&s=sAyFaFwMY8DW2IeEuGkCVee-HPTMZkKhgegRy9V10JY&e=>
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:36 CST