[gmx-users] Re: gmx-users Digest, Vol 80, Issue 88

[Thomas Schlesier]

The distance between the com of the pulled group and the dummy particle 
/ spring you have implicit in pullf.xvg (implicit since, it's the 
distance modified by the force constant of the spring, to get the force).

I think the best one can do (to see which are which distances and how 
they are related to each other), is to run a small simulation and look 
into the distances with a plotting program:

For example if you use 'pull_geometry=position' you have:
REF position of the reference group - in pullx.xvg
RP  distance between reference and pulled group - also in pull.xvg (this 
distance you can also get with g_dist and using both groups as input)
PS  distance between pulled group and spring - in pullf.xvg (just divide 
with the force constant)
RS  distance between reference group and spring (initial distance 
between spring and reference group and spring + time * pulling_velocity 
(modified by the pull_vector))

Since you know all three distances, you can calculated one of the with 
the two others and look if they are the same.
So RP + PS = RS etc.

With 'pull_geometry=direction' it should be similar simple, but i think 
with 'pull_geometry=distance' it becomes nastier, if your molecule/s 
start to rotate and the pulling_vector doesn't remain constant.

Greetings
Thomas


>
> Message: 3
> Date: Mon, 13 Dec 2010 18:04:28 +0100
> From: Christian M?cksch<muecksch at rhrk.uni-kl.de>
> Subject: [gmx-users] Question about COM-Pulling
> To: gmx-users at gromacs.org
> Message-ID:<4D06521C.1030601 at rhrk.uni-kl.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
>
> this is a more general question.
>
> I thought that in analogy to an AFM-experiment a "dummy"-particle is placed
> at a certain distance from the center of mass of the pull group (compare
> figure 6.1 in the manual).
> The force is then calculated as the displacement between the pulled atom
> and the
> "dummy"-particle. So if this is true which I'm not sure of,
> I was wondering why the position of this "dummy"-particle is not plotted.
>
> Or does this umbrella pulling work in a different way? How is the force
> calculated?
>
> Thanks a lot,
> Christian
>
> ----------------------------------------------------------------------
> The position of the reference group and the displacement of the pulled
> group from the reference group should be printed (although perhaps
> without the reference position if you are using absolute coordinate
> pulling, which is not recommended anyhow).
>
> If you want some better advice, please be more specific and include
> cut and paste sections saying "I expected X at Y, but it was not in
> the file Z.xvg". you should also include your pull-code .mdp options
> and your grompp and mdrun commands.
>
> Chris.
>
> -- original message --
>
> Dear users,
>
> I've got a short question regarding com-pulling. From what I understand
> Umbrella pulling is the same as AFM pulling using a harmonic potential.
>
> Why is the position of the spring in the pullx.xvg not printed? One can
> only find the vector between both pull groups. I looked into older
> Gromacs manuals and in versions<  4 it seems as if this data is printed
> to the pullx.xvg file or something similar.
>
> With kind regards,
> Christian
>