[gmx-users] Question about COM-Pulling

[Christian Mücksch]

>  Here you have time, the z position of your reference group and the
>  difference along z between your pull group and your reference group.
>  There is no "dummy particle" as the spring extends between the
>  "reference" group at z=1.1675 and the "pull" group, which in the first
>  frame is located at z=1.1675 + 3.47701.
>
>  I have used the pull code since v3.3.1 and I do not recall there ever
>  being a dummy particle when using:
>
>  pull = umbrella
>  pull_geometry = distance
>
>  It is the distance of the restraint that changes over time in your setup.

Sorry to ask again but I'm a bit confused. I thought that a spring (harmonic potential)
is connected to the pull-group (by "dummy-particle" I meant the top of the spring=zspring)
and then moved at a certain pull_rate in the desired direction.

If the spring extends from the pull-group to the reference group and the reference group stays in place while the pull-group is moved away,
then the spring would extend and extend and therefore the force rise and rise. What obvious fact am I missing?

Is there a difference between AFM pulling and Umbrella pulling?


On 10-12-13 01:29 PM,gmx-users-request at gromacs.org  <http://lists.gromacs.org/mailman/listinfo/gmx-users>  wrote:
>/  ubject: [gmx-users] Question about COM-Pulling
/>/  To: MAILINGLIST GROMACS<gmx-users at gromacs.org  <http://lists.gromacs.org/mailman/listinfo/gmx-users>>
/>/  Message-ID:<4D065C09.4020809 at rhrk.uni-kl.de  <http://lists.gromacs.org/mailman/listinfo/gmx-users>>
/>/  Content-Type: text/plain; charset=UTF-8; format=flowed
/>/
/>/  Hi,
/>/
/>/  although this is not relevant to my previous question:
/
It is indeed relevant.

>/  I used mdrun like this:
/>/
/>/  mdrun -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr
/>/  -g pull.log -px pull_dist.xvg -pf pull_force.xvg
/>/
/>/  With an input-file like this:
/>/
/>/  ------------------------------------------------
/>/  ; Run-Parameter
/>/  integrator = md
/>/  dt = 0.002
/>/  nsteps = 1000000
/>/
/>/  ; OUTPUT CONTROL OPTIONS
/>/  nstxout = 5000
/>/  nstvout = 5000
/>/  nstfout = 5000
/>/  nstlog = 5000
/>/  nstenergy = 5000
/>/
/>/  pull_nstxout = 100 ;
/>/  pull_nstfout = 100 ;
/>/
/>/  rlist = 1.2
/>/  ns_type = grid
/>/  coulombtype = PME-Switch
/>/  rcoulomb = 1.0
/>/  vdw-type = shift
/>/  rvdw = 1.0
/>/  rvdw_switch = 0.9
/>/  pbc = xyz
/>/
/>/  tcoupl = V-rescale
/>/  tc-grps = Protein Non-Protein
/>/  tau_t = 0.1 0.1
/>/  ref_t = 300 300
/>/
/>/  pcoupl = Berendsen
/>/  pcoupltype = isotropic
/>/  tau_p = 2
/>/  ref_p = 1
/>/  compressibility = 4.5e-5
/>/
/>/  DispCorr = EnerPres
/>/  continuation = yes
/>/
/>/  constraint_algorithm = lincs
/>/  constraints = all-bonds
/>/
/>/  pull = umbrella
/>/  pull_geometry = distance
/>/  pull_dim = N N Y
/>/  pull_start = yes
/>/  pull_ngroups = 1
/>/  pull_group0 = reference
/>/  pull_group1 = pull
/>/  pull_rate1 = 0.01
/>/  pull_k1 = 1000
/>/  ------------------------------------------------
/>/
/>/  ...I get an output for pull_dist.xvg which looks sth. like this:
/>/
/>/  ------------------------------------------------
/>/  # This file was created Fri Nov 26 16:22:53 2010
/>/  # by the following command:
/>/  # /mnt/nas1/c_muecksch/GROMACS_4.5.3/bin/mdrun_mpi_4.5.3_s -v -s
/>/  pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log
/>/  -px pull_dist.xvg -pf pull_force.xvg
/>/  #
/>/  # mdrun_mpi_4.5.3_s is part of G R O M A C S:
/>/  #
/>/  # Grunge ROck MAChoS
/>/  #
/>/  @ title "Pull COM"
/>/  @ xaxis label "Time (ps)"
/>/  @ yaxis label "Position (nm)"
/>/  @TYPE xy
/>/  @ view 0.15, 0.15, 0.75, 0.85
/>/  @ legend on
/>/  @ legend box on
/>/  @ legend loctype view
/>/  @ legend 0.78, 0.8
/>/  @ legend length 2
/>/  @ s0 legend "0 Z"
/>/  @ s1 legend "1 dZ"
/>/  0.0000 1.1675 3.47701
/>/  0.2000 1.1675 3.48043
/>/  0.4000 1.1675 3.4795
/>/  0.6000 1.1675 3.48214
/>/  0.8000 1.1675 3.4869
/>/
/>/  and so on
/
Here you have time, the z position of your reference group and the
difference along z between your pull group and your reference group.
There is no "dummy particle" as the spring extends between the
"reference" group at z=1.1675 and the "pull" group, which in the first
frame is located at z=1.1675 + 3.47701.

I have used the pull code since v3.3.1 and I do not recall there ever
being a dummy particle when using:

pull = umbrella
pull_geometry = distance

It is the distance of the restraint that changes over time in your setup.

Chris.



>/  ------------------------------------------------
/>/
/>/  In this pull_dist.xvg there is no position of a "dummy"-particle that is
/>/  connected via a harmonic potential to the pull group (as described in
/>/  GrubmuÌ^ller, Helmut ; Heymann, Berthold ; Tavan, Paul: Ligand Binding:
/>/  Molecular Mechanics Calculation of the StreptavidinâEUR"Biotin Rupture
/>/  Force. In: Science 271 (1996))
/>/
/>/  In older version of Gromacs I believe that this was the case. Has the
/>/  method changed? How is the force calculated if not by the displacment of the
/>/  "dummy"-particle. I just wanted to know how the afm pulling in gromacs
/>/  is achieved without having to look in the source-code.
/>/
/>/  Thx,
/>/  Christian
/>/
/>/
/>/  ---------------------------------------------------------------------------------------
/>/  Dear Christian:
/>/
/>/  As per my original comments, please provide a .mdp file, sample
/>/  output, and all the other things that I asked for.
/>/
/>/  Chris.
/>/
/>/  --original message--
/>/
/>/  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
/>/
/

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