From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jun 05 2013 - 17:17:04 CDT
It is a generalized force: so, not a Cartesian vector.
On Wed, Jun 5, 2013 at 6:14 PM, Ivan Mikhaylov <ivan.mikhaylov_at_gmail.com>wrote:
> 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,
> On Wed, Jun 5, 2013 at 5:49 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> > If you introduced a harmonic restraint, distance*forceConstant is equal
> > the force that is applied by you to the system, aka the "applied force".
> > 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
> > 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
> > 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
> > 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
> > 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:
> >> 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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