[gmx-users] Re: how is the pulling force measured
jasonzhu925 at gmail.com
Wed Aug 7 20:56:07 CEST 2013
I would like to give my understanding of the pulling method. I don't look
into the code either. I am not sure if my understanding is right. Any
correction is welcome.
I think the reference point connecting with the pulled group by spring is an
COM offset of the reference group. The reference point in fact represents
the reference group. Any force induced by spring acts on the pulled group,
meanwhile its counter force acts on the reference point (or the reference
group). That is why the reference group and the pulled group can be treated
equivalently if the simulation system consists of one reference group and
one pulled group (see Gromacs Manual). If we don't fix the reference group,
the COM of system is stationary.
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