Namd-I: A question about constant force pulling of a group of atoms

From: Ye Yang (knightyangpku_at_gmail.com)
Date: Thu Sep 01 2011 - 10:16:18 CDT

Hi, everyone:
       I am trying to pull a group of atoms with constant force. But I am
not sure in this case if each atom in the group sense a pulling force or the
center of mass sense the the pulling force.
       It is straightforward for constant velocity, which is actually
pulling the center of mass.
       However, in constant force, since you define the pulling force in the
reference file, if I define a group of atoms (let's say two atoms) with the
same force 500pN, what will be the result? Only the force on the center of
mass of this? Or each one of the atom sense this force (in this case the
group is sensing twice of the force 1000pN)
       Right now, I am trying to pull a double strand dna with constant
force, yet I am not sure if I should just pull the ends of one strand or two
strands.
       Also, if I define different pulling force for these two atoms, what
will be the net force of the group? Is it just the summation of the two
forces?
       Thank you very much.

Ye

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