**From:** Jérôme Hénin (*jerome.henin_at_ibpc.fr*)

**Date:** Thu Aug 31 2017 - 17:36:54 CDT

**Next message:**Vermaas, Joshua: "Re: error - atom type not in psf"**Previous message:**Ben Adams: "problem with minimization and calculation of force on a fixed atom"**In reply to:**Ben Adams: "problem with minimization and calculation of force on a fixed atom"**Next in thread:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Reply:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

I've been told of a certain command named fixedAtomsForces that sounds just

like what you need :-)

Jerome

On 1 September 2017 at 00:03, Ben Adams <benny.adams1993_at_gmail.com> wrote:

*> Dear NAMD users,
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*>
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*> I want to calculate forces on a few constrained atoms while I'm doing
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*> merely energy minimization. I used colvars with harmonic restraints and
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*> obtained force based on the distance of the atom of interest to a specified
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*> Center value. But the minimization causes dramatic fluctuations on
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*> calculation of force. Changing the force constant, minimization options
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*> mentioned in tutorial don't help that much. and the results are not even
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*> reproducible.
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*> An alternative way would be to freeze that atom and calculate the force
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*> directly. But using the 'fixedAtoms' option leaves the force at the atom
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*> equal to zero and do not allow to extract its value.
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*> Is there any other way to freeze an atom while the force on it is being
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*> calculated?
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*> Or is there anyway to make minimization more stable when a colvar
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*> constraint is present?
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*>
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*> Thanks in advance,
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*>
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*>
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*>
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**Next message:**Vermaas, Joshua: "Re: error - atom type not in psf"**Previous message:**Ben Adams: "problem with minimization and calculation of force on a fixed atom"**In reply to:**Ben Adams: "problem with minimization and calculation of force on a fixed atom"**Next in thread:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Reply:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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