**From:** Ben Adams (*benny.adams1993_at_gmail.com*)

**Date:** Fri Sep 01 2017 - 11:01:49 CDT

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Is there any way to out put the constraint force separately?

On Fri, Sep 1, 2017 at 10:48 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

*> Indeed... What I suspect might be happening here is that the constraint
*

*> force gets included in the reported total force, which adds up to zero.
*

*>
*

*> Jerome
*

*>
*

*> On 1 September 2017 at 17:36, Ben Adams <benny.adams1993_at_gmail.com> wrote:
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*>
*

*>>
*

*>> Thanks but even when I use fixedAtomsForces it still returns zeros. For
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*>> example here atom 2431 is frozen but the force output is zeros:
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*>>
*

*>>
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*>> fixedAtoms on
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*>>
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*>> fixedAtomsForces on
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*>>
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*>> fixedAtomsFile fix.pdb
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*>>
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*>> fixedAtomsCol B
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*>>
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*>> tclForces on
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*>>
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*>> tclForcesScript {
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*>>
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*>>
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*>> set nter [addgroup {1}]
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*>>
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*>> set cter [addgroup {2431}]
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*>>
*

*>> proc calcforces {} {
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*>>
*

*>> global cter
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*>>
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*>> loadcoords coor
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*>>
*

*>> enabletotalforces
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*>>
*

*>> if {[getstep] > 0} {
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*>>
*

*>> loadtotalforces forces
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*>>
*

*>> print $forces($nter)
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*>>
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*>> # print cter= $forces(cter)
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*>>
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*>> }
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*>>
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*>> }
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*>>
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*>> }
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*>>
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*>> On Thu, Aug 31, 2017 at 5:36 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> w
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*>> rote:
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*>>
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*>>> I've been told of a certain command named fixedAtomsForces that sounds
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*>>> just like what you need :-)
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*>>>
*

*>>> Jerome
*

*>>>
*

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

*>>>> Dear NAMD users,
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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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*>>>>
*

*>>>> Thanks in advance,
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>
*

*>
*

**Next message:**Jérôme Hénin: "Re: problem with minimization and calculation of force on a fixed atom"**Previous message:**Jérôme Hénin: "Re: problem with minimization and calculation of force on a fixed atom"**In reply to:**Jérôme Hénin: "Re: problem with minimization and calculation of force on a fixed atom"**Next in thread:**Jérôme Hénin: "Re: problem with minimization and calculation of force on a fixed atom"**Reply:**Jérôme Hénin: "Re: problem with minimization and calculation of force on a fixed atom"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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