[gmx-users] pullx/pullf and COM energy

Alex nedomacho at gmail.com
Sat May 13 09:26:48 CEST 2017

Hi all,

I am slowly pulling a single ion (restrained in-plane) along the Z 
direction at a constant rate via a spring (what you call umbrella). At 
the moment, the physics probably doesn't matter, but my question will be 
clear in a moment and yes, I am aware of threads like 

It is my understanding that pullf.xvg reports the force exerted by the 
spring upon the ion, i.e. the k(vt-x(t)), where v is the pulling rate 
and k is the puller spring constant. It is also my understanding that 
the COM pulling energy (if you apply 'gmx energy' to your energy output) 
reports the energy stored in that spring. Seems elementary. It would 
follow that if I were to take the force data from pullf.xvg and 
integrate it, I would indeed obtain the COM energy.

The dumb integral is f(x)vdt, while the more appropriate approach is 
f(x)dx, where dx is obtained from pullx.xvg for every t. Makes little 
difference -- in my case vt and x(t) are always very close and I get 
very similar results from the two integrals, aside from noise. However, 
both of them are also entirely different from what I get for the COM 
pull energy from the energy utility.

Can someone help solve this mystery?

Thank you,


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