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

**Date:** Fri Sep 01 2017 - 10:48:49 CDT

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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:

*>
*

*> 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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*>
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*> proc calcforces {} {
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*>
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*> global cter
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*>
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*> loadcoords coor
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*>
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*> enabletotalforces
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*>
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*> if {[getstep] > 0} {
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*>
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*> loadtotalforces forces
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*>
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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>
*

*> wrote:
*

*>
*

*>> 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:
*

*>>
*

*>>> 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?
*

*>>> 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,
*

*>>>
*

*>>>
*

*>>>
*

*>>
*

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