[gmx-users] work from pulling simulation
Daniel S. Han
dsh2002 at med.cornell.edu
Thu Dec 4 02:36:08 CET 2008
I am performing steered MD simulations using the pull code in
1-Dimension (z) and I'd like to calculate the work done on my system (in
the z-direction) by the pulling spring.
If my output PDO pulling file looks something like this:
Time Z_pulled_group Z_bead
0 0 0
1 .5 1
2 1 2
Then my forces and work should be this?
Time dZ Spring Force Work_on_system
0 0 0 * k 0 * 0 * k ???
1 .5 .5 * k .5 * .5 * k ???
2 1 1 * k 1 * 1 * k ???
dZ = (Z_bead-Z_pulled_group)
F = k*dz
W = F*dz
Originally, I thought it would be more accurate to get the work by using an average force.
For example, at t=1,
W = (F(t=1)+F(t=0))/2 * dZ(t=1),
but the results obtained this way seem to be worse -- meaning they were very different than what I expected in my control systems.
If someone could please comment on whether this seems to be the correct/incorrect way to calculate things, I would appreciate it.
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