From: Ivan Mikhaylov (ivan.mikhaylov_at_gmail.com)
Date: Wed Jun 05 2013 - 17:14:50 CDT
Thank you for answering my questions. Only one left. According to the
eq(50), the force from other atoms is vector. Is not it? What do
negative and positive values mean?
With best regards,
IM
On Wed, Jun 5, 2013 at 5:49 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
> If you introduced a harmonic restraint, distance*forceConstant is equal to
> the force that is applied by you to the system, aka the "applied force". If
> you want to measure the force on your variable from all the atoms in the
> system, that is called the "system" force: it does not contain the applied
> force, so don't expect it to change with the force constant.
>
> The equation you linked comes from an article (Ciccotti et al), which you
> could always check out for more details. If the article is also unclear, I
> am sure that the first author would be delighted to hear and very much open
> to provide further explanations.
>
> The reason why the first system force is zero is a subtle technical one.
> Due to the design of NAMD, collective variables and their derived quantities
> are calculated before all the atom-atom forces are completely calculated.
> So the system force is the one from the previous integration step, which
> doesn't exist at time step 0. If you do a short test with
> colvarsTrajFrequency = 1, you'll see that starting from step 1 the data is
> complete.
>
> Cheers
> Giacomo
>
>
>
>
> On Wed, Jun 5, 2013 at 5:28 PM, Ivan Mikhaylov <ivan.mikhaylov_at_gmail.com>
> wrote:
>>
>> I defined a colvar "distance" and "forceConstant 10.0" asking for
>> "oneSiteSystemForce" printing.
>> I have an output in *.colvars.traj as follows:
>>
>> # step 1st-colvar fs_1st-colvar
>> 0 2.70639531217785e+00 0.00000000000000e+00
>> 1000 2.76803828316001e+00 2.49728670452675e+00
>> .... ........ ...............
>> 7000 3.14579942428557e+00 -3.41836799520439e+01
>>
>> As you see, the very first force is zero and there are positive and
>> negative values in the third column for the forces.
>>
>> Equation (50) in section 10.3.1:
>> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node56.html#eq:gradient_vector
>> does not really help, because it is unclear.
>>
>> I thought that the force should be equal to distance*forceConstant.
>> Why is it not?
>>
>> Could you tell me, please, what "outputSystemForce" outputs?
>>
>
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