[gmx-users] Re: Fwd: about the pulling

[Justin A. Lemkul]

Tom wrote:
> Justin
> 
> you have good experience of pulling.
> 
> If you have time, please help with this publling problem:
> abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot!
> 

I already commented:

http://lists.gromacs.org/pipermail/gmx-users/2011-October/065226.html

> i am pulling A object towards B along z-axis. But system
> has pbc on x, y and z. Is it because of the pbc image of B
> object that make grmx confused to report the sign.
> 

Likely.  If your box is not greater than about 16.3 nm in Z, then you'll have 
this problem.

> In my system, A should be on the top of B in z-axis, but i just noticed
> that at the intial step: 1dZ has been negative already.
> It seems the system use the PBC image (in z-axis) of the reference object B
>  to cacluate 1dZ, right?

Sounds right.

-Justin

> --------------------------------------
> @    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  0.77622 -8.13474
> ------------------------------------
> 
> Thanks a lot for the help!
> 
> Tom
> 
> ---------- Forwarded message ----------
> From: Tom <dnaafm at gmail.com>
> Date: Sun, 16 Oct 2011 23:02:09 +0800
> Subject: about the pulling
> To: gmx-users <gmx-users at gromacs.org>
> 
> Dear Gromacs Users or Developers,
> 
> I am using the pulling the COM of object A towards B using:
> ---------------------------------
> pull                     = umbrella
> pull_geometry            = distance
> pull_dim                 = N N Y
> pull_start               = yes
> pull_ngroups             = 1
> pull_group0              = B
> pull_group1              = A
> pull_rate1               = -0.00005714
> pull_k1                  = 5000
> -------------------------------
> On the output file of pullx.xvg,  the sign of dZ
> has been changed from negative to posivitve
> or vice vrsa in all sudden. What does it mean?
> 
> The following is an example:
> 
> @    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"
> 
> ---------------------------------------------------
> 173.7400        0.77622 8.14856
> 173.7500        0.77622 8.14897
> 173.7600        0.77622 8.14938
> 173.7700        0.77622 8.14977
> 173.7800        0.77622 -8.14987
> 173.7900        0.77622 -8.14954
> 173.8000        0.77622 -8.14924
> 173.8100        0.77622 -8.14895
> ------------------------------------
> 
> 
> Thanks a lot for the information!
> 
> Thanks,
> 
> Tom
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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