[gmx-users] Questions to pullx.xvg

Berk Hess gmx3 at hotmail.com
Wed May 6 15:57:16 CEST 2009


You are completely right.
This should have been documented somewhere.
But I changed this after the 4.0 release in on of the minor releases,
therefore this could not be documented.
In pullx.xvg X 0 means the coordinate(s) of group 0 and dX 1 the vector
from group 0 to group 1.


> Date: Wed, 6 May 2009 10:56:29 +0200
> From: schlesi at uni-mainz.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Questions to pullx.xvg
> Hi all,
> what are the meanings of the columns X and dX? From the manual i think
> the first column X should be the position of the pull-group. But in my
> case it is the position of the reference group, so i'm a little bit
> troubled. And what is dX? For me it looks that this is the vector from
> the reference-group to the pull-group. And then the forces in pullf.xvg
> were calculated with:
> F(t)= k*[S - (RP(t)-RP(0))]
> Where F is the force, S the vector from the reference-group to the
> spring (= pull_init + t * pull_rate * pull_vec) and RP the vector from
> the reference-group to the pull-group and t the time.
> (I used the umbrella pulling, with pull-geometry = position)
> Am i right?
> Greetings Thomas
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