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