[gmx-users] work from pulling simulation

[Daniel S. Han]

Hello GMXers,

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  ???	

where 
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.
Thanks, 
Danny.