Re: problem with minimization and calculation of force on a fixed atom

From: Ben Adams (
Date: Fri Sep 01 2017 - 10:36:21 CDT

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


if {[getstep] > 0} {

    loadtotalforces forces

    print $forces($nter)

# print cter= $forces(cter)




On Thu, Aug 31, 2017 at 5:36 PM, Jérôme Hénin <> wrote:

> 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 <> wrote:
>> Dear NAMD users,
>> I want to calculate forces on a few constrained atoms while I'm doing
>> merely energy minimization. I used colvars with harmonic restraints and
>> obtained force based on the distance of the atom of interest to a specified
>> Center value. But the minimization causes dramatic fluctuations on
>> calculation of force. Changing the force constant, minimization options
>> mentioned in tutorial don't help that much. and the results are not even
>> reproducible.
>> An alternative way would be to freeze that atom and calculate the force
>> directly. But using the 'fixedAtoms' option leaves the force at the atom
>> 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
>> calculated?
>> Or is there anyway to make minimization more stable when a colvar
>> constraint is present?
>> Thanks in advance,

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