[gmx-users] Questions to pullx.xvg
schlesi at uni-mainz.de
Wed May 6 16:22:15 CEST 2009
thanks for the clarification.
> 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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