[gmx-users] Re: pullx file content with pull_geometry = position

[Justin Lemkul]

On 6/6/13 5:17 AM, Bastien Loubet wrote:
> I update the post to say that we tried to make a rerun of the trajectory on
> our local machine and the output of the pullx.xvg file (created with the
> option -px of mdrun) is:
>
> ************************************************
> # This file was created Wed Jun  5 12:15:49 2013
> # by the following command:
> # mdrun -s ../conf10.tpr -rerun ../conf10.xtc -px pullx_conf10.xvg -pf
> pullf_conf10.xvg -nt 6 -v
> #
> # mdrun is part of G R O M A C S:
> #
> # Gravel Rubs Often Many Awfully Cauterized Sores
> #
> @    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 X"
> @ s1 legend "0 Y"
> @ s2 legend "0 Z"
> @ s3 legend "1 dX"
> @ s4 legend "1 dY"
> @ s5 legend "1 dZ"
> 0.0000  3.47835 5.10501 11.644  -0.378345       1.13499 1.73604
> 20.0000 3.47852 5.12016 11.6554 -0.446518       1.07184 1.69255
> 40.0000 3.49803 5.12013 11.6612 -0.350032       1.12387 1.75475
> (...)
> **********************************************
>
> The output of the pullx.xvg file is indeed the distance between the two pull
> groups, but this is very different numbers than the one obtained  during the
> simulation on a cluster (see above post).
> So the question stand what are the numbers given in the pullx.xvg file
> created during the original simulation ?
>

http://lists.gromacs.org/pipermail/gmx-users/2009-June/042887.html

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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