[gmx-users] re:re:desorting

David van der Spoel spoel at xray.bmc.uu.se
Mon Oct 31 14:08:34 CET 2005

On Mon, 2005-10-31 at 14:43 +0200, aneamtu at iasi.mednet.ro wrote:
> Thanks for the reply
> but I really need to desort the trajecories because my simulation is made of several runs. Every run was made with -sort and -shuffle option to gain performance by resorting the molecules according to their OX coordinate. Otherwise, becuse my molecules diffuse a lot in the course of the simulation, the performance will decrease over time. When I cat the trajectory files the order of molecules from one file do not correspond to ones in the others. This affects the trjconv option -nojump and other analysis tools like VMD trajectory smoothing.
> Is there any solution to this problem?

Sorry, no.

You'll have to write a script or program yourself. This will be fixed in
the 4.0 release.
> Thanks,
> Andrei
> ------------------------
> Dr. Andrei Neamtu, M.D., Assistant Researcher
> Dept. of Biophysiscs
> University of Medicine and Pharmacy "Gr. T. Popa" Iasi
> ------------------------
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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