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

**Date:** Fri Sep 01 2017 - 10:36:21 CDT

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Thanks but even when I use fixedAtomsForces it still returns zeros. For

example here atom 2431 is frozen but the force output is zeros:

fixedAtoms on

fixedAtomsForces on

fixedAtomsFile fix.pdb

fixedAtomsCol B

tclForces on

tclForcesScript {

set nter [addgroup {1}]

set cter [addgroup {2431}]

proc calcforces {} {

global cter

loadcoords coor

enabletotalforces

if {[getstep] > 0} {

loadtotalforces forces

print $forces($nter)

# print cter= $forces(cter)

}

}

}

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
*

*> just like what you need :-)
*

*>
*

*> Jerome
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*>
*

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

*>
*

*>> Dear NAMD users,
*

*>>
*

*>> 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.
*

*>> 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.
*

*>> 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,
*

*>>
*

*>>
*

*>>
*

*>
*

**Next message:**Jérôme Hénin: "Re: problem with minimization and calculation of force on a fixed atom"**Previous message:**Norman Geist: "AW: NAMD-2.12 CUDA2 and PMECUDA problems"**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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