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

From: Ben Adams (benny.adams1993_at_gmail.com)
Date: Fri Sep 01 2017 - 11:01:49 CDT

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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