[gmx-users] trajectory not seen

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 31 02:52:10 CET 2005

On Mon, 2005-01-31 at 12:49 +0530, Jaimin Shah wrote:
> Dear all,
> I have done an mdrun of my protein, and then I put ngmx to view the
> dynamics. It shows 44 ps on clicking "animate" but it does not move on
> forwarding or reversing.
> Also, please tell me how do i get the coordinates of all the different
> conformations of the molecule in the trajectory so that I can do docking
> simulations.
run gmxcheck to see how many frames there are, use trjconv to output pdb
files from yourtrajectory
> Thanking you in advance,
> Sincerely,
> Jaimin Shah
> Junior Research Fellow
> Dr. Dulal Panda's Laboratory
> School of Biosciences & Bioengineering
> I.I.T. Bombay
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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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