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<pre>> 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, <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">gmx-users-request at gromacs.org</a> wrote:
><i> ubject: [gmx-users] Question about COM-Pulling
</i>><i> To: MAILINGLIST GROMACS<<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">gmx-users at gromacs.org</a>>
</i>><i> Message-ID:<<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">4D065C09.4020809 at rhrk.uni-kl.de</a>>
</i>><i> Content-Type: text/plain; charset=UTF-8; format=flowed
</i>><i>
</i>><i> Hi,
</i>><i>
</i>><i> although this is not relevant to my previous question:
</i>
It is indeed relevant.
><i> I used mdrun like this:
</i>><i>
</i>><i> mdrun -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr
</i>><i> -g pull.log -px pull_dist.xvg -pf pull_force.xvg
</i>><i>
</i>><i> With an input-file like this:
</i>><i>
</i>><i> ------------------------------------------------
</i>><i> ; Run-Parameter
</i>><i> integrator = md
</i>><i> dt = 0.002
</i>><i> nsteps = 1000000
</i>><i>
</i>><i> ; OUTPUT CONTROL OPTIONS
</i>><i> nstxout = 5000
</i>><i> nstvout = 5000
</i>><i> nstfout = 5000
</i>><i> nstlog = 5000
</i>><i> nstenergy = 5000
</i>><i>
</i>><i> pull_nstxout = 100 ;
</i>><i> pull_nstfout = 100 ;
</i>><i>
</i>><i> rlist = 1.2
</i>><i> ns_type = grid
</i>><i> coulombtype = PME-Switch
</i>><i> rcoulomb = 1.0
</i>><i> vdw-type = shift
</i>><i> rvdw = 1.0
</i>><i> rvdw_switch = 0.9
</i>><i> pbc = xyz
</i>><i>
</i>><i> tcoupl = V-rescale
</i>><i> tc-grps = Protein Non-Protein
</i>><i> tau_t = 0.1 0.1
</i>><i> ref_t = 300 300
</i>><i>
</i>><i> pcoupl = Berendsen
</i>><i> pcoupltype = isotropic
</i>><i> tau_p = 2
</i>><i> ref_p = 1
</i>><i> compressibility = 4.5e-5
</i>><i>
</i>><i> DispCorr = EnerPres
</i>><i> continuation = yes
</i>><i>
</i>><i> constraint_algorithm = lincs
</i>><i> constraints = all-bonds
</i>><i>
</i>><i> pull = umbrella
</i>><i> pull_geometry = distance
</i>><i> pull_dim = N N Y
</i>><i> pull_start = yes
</i>><i> pull_ngroups = 1
</i>><i> pull_group0 = reference
</i>><i> pull_group1 = pull
</i>><i> pull_rate1 = 0.01
</i>><i> pull_k1 = 1000
</i>><i> ------------------------------------------------
</i>><i>
</i>><i> ...I get an output for pull_dist.xvg which looks sth. like this:
</i>><i>
</i>><i> ------------------------------------------------
</i>><i> # This file was created Fri Nov 26 16:22:53 2010
</i>><i> # by the following command:
</i>><i> # /mnt/nas1/c_muecksch/GROMACS_4.5.3/bin/mdrun_mpi_4.5.3_s -v -s
</i>><i> pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log
</i>><i> -px pull_dist.xvg -pf pull_force.xvg
</i>><i> #
</i>><i> # mdrun_mpi_4.5.3_s is part of G R O M A C S:
</i>><i> #
</i>><i> # Grunge ROck MAChoS
</i>><i> #
</i>><i> @ title "Pull COM"
</i>><i> @ xaxis label "Time (ps)"
</i>><i> @ yaxis label "Position (nm)"
</i>><i> @TYPE xy
</i>><i> @ view 0.15, 0.15, 0.75, 0.85
</i>><i> @ legend on
</i>><i> @ legend box on
</i>><i> @ legend loctype view
</i>><i> @ legend 0.78, 0.8
</i>><i> @ legend length 2
</i>><i> @ s0 legend "0 Z"
</i>><i> @ s1 legend "1 dZ"
</i>><i> 0.0000 1.1675 3.47701
</i>><i> 0.2000 1.1675 3.48043
</i>><i> 0.4000 1.1675 3.4795
</i>><i> 0.6000 1.1675 3.48214
</i>><i> 0.8000 1.1675 3.4869
</i>><i>
</i>><i> and so on
</i>
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.
><i> ------------------------------------------------
</i>><i>
</i>><i> In this pull_dist.xvg there is no position of a "dummy"-particle that is
</i>><i> connected via a harmonic potential to the pull group (as described in
</i>><i> Grubmüller, Helmut ; Heymann, Berthold ; Tavan, Paul: Ligand Binding:
</i>><i> Molecular Mechanics Calculation of the Streptavidin–Biotin Rupture
</i>><i> Force. In: Science 271 (1996))
</i>><i>
</i>><i> In older version of Gromacs I believe that this was the case. Has the
</i>><i> method changed? How is the force calculated if not by the displacment of the
</i>><i> "dummy"-particle. I just wanted to know how the afm pulling in gromacs
</i>><i> is achieved without having to look in the source-code.
</i>><i>
</i>><i> Thx,
</i>><i> Christian
</i>><i>
</i>><i>
</i>><i> ---------------------------------------------------------------------------------------
</i>><i> Dear Christian:
</i>><i>
</i>><i> As per my original comments, please provide a .mdp file, sample
</i>><i> output, and all the other things that I asked for.
</i>><i>
</i>><i> Chris.
</i>><i>
</i>><i> --original message--
</i>><i>
</i>><i> this is a more general question.
</i>><i>
</i>><i> I thought that in analogy to an AFM-experiment a "dummy"-particle is placed
</i>><i> at a certain distance from the center of mass of the pull group (compare
</i>><i> figure 6.1 in the manual).
</i>><i> The force is then calculated as the displacement between the pulled atom
</i>><i> and the
</i>><i> "dummy"-particle. So if this is true which I'm not sure of,
</i>><i> I was wondering why the position of this "dummy"-particle is not plotted.
</i>><i>
</i>><i> Or does this umbrella pulling work in a different way? How is the force
</i>><i> calculated?
</i>><i>
</i>><i> Thanks a lot,
</i>><i> Christian
</i>><i>
</i>><i> ----------------------------------------------------------------------
</i>><i> The position of the reference group and the displacement of the pulled
</i>><i> group from the reference group should be printed (although perhaps
</i>><i> without the reference position if you are using absolute coordinate
</i>><i> pulling, which is not recommended anyhow).
</i>><i>
</i>><i> If you want some better advice, please be more specific and include
</i>><i> cut and paste sections saying "I expected X at Y, but it was not in
</i>><i> the file Z.xvg". you should also include your pull-code .mdp options
</i>><i> and your grompp and mdrun commands.
</i>><i>
</i>><i> Chris.
</i>><i>
</i>><i> -- original message --
</i>><i>
</i>><i> Dear users,
</i>><i>
</i>><i> I've got a short question regarding com-pulling. From what I understand
</i>><i> Umbrella pulling is the same as AFM pulling using a harmonic potential.
</i>><i>
</i>><i> Why is the position of the spring in the pullx.xvg not printed? One can
</i>><i> only find the vector between both pull groups. I looked into older
</i>><i> Gromacs manuals and in versions< 4 it seems as if this data is printed
</i>><i> to the pullx.xvg file or something similar.
</i>><i>
</i>><i> With kind regards,
</i>><i> Christian
</i>><i>
</i></pre>
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