[gmx-users] pullx/pullf and COM energy
Alex
nedomacho at gmail.com
Sat May 13 09:38:46 CEST 2017
Ah, nevermind -- problem solved. The proper integral is of course wrt
d(vt-x), which gives a fairly noisy version of the COM energy.
On 5/13/2017 1:26 AM, Alex wrote:
> 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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