From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Sep 01 2017 - 11:02:52 CDT
Actually, looking into the code behind this, I think there is a way. The
force gets zeroed out arbitrarily in ComputeGlobal.C, line 374:
if ( fixedAtomsOn && atoms[i].atomFixed ) f_sum = 0.;
Commenting out that line and rebuilding NAMD seems to do the job for me.
Please test this, and if the force values you obtain seem correct, I'll
submit a patch.
Jerome
On 1 September 2017 at 18:01, Ben Adams <benny.adams1993_at_gmail.com> wrote:
> Is there any way to out put the constraint force separately?
>
> On Fri, Sep 1, 2017 at 10:48 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> 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> w
>>> rote:
>>>
>>>> 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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