From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Sep 01 2017 - 10:48:49 CDT
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
> 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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