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<mueck...@rhrk.uni-kl.de>
Subject: [gmx-users] Question about COM-Pulling
To: gmx-users@gromacs.org
Message-ID:<4d06521c.1030...@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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
