**From:** Brian Radak (*bradak_at_anl.gov*)

**Date:** Tue Sep 19 2017 - 08:30:20 CDT

**Next message:**Victoria Lim: "Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option?"**Previous message:**Victoria Lim: "What is the exact form of the harmonic potential used by the NAMD "constraints" option?"**In reply to:**Victoria Lim: "What is the exact form of the harmonic potential used by the NAMD "constraints" option?"**Next in thread:**Victoria Lim: "Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option?"**Reply:**Victoria Lim: "Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
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*> realize the "extraBonds" option does /not/ contain this factor,
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*> whereas the harmonic potential in the colvars module does have the
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*> 1/2. However, I could not find an explicit formula for the constraints
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*> option.
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*>
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*> 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

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