[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
http://thread.gmane.org/gmane.science.biology.gromacs.user/77762.
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,
Alex
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