[gmx-users] -b option for g_order
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 1 16:29:30 CET 2005
Beate Griepernau wrote:
>I did a simulation of a membrane over a time period of 50ns writing out
>coordinates every picosecond.
>Next I edited the .xtc-file to get a new .xtc file keeping only the
>data of every 10th step using trjconv and option -skip.
>On this new .xtc-file I applied g_order with different beginning and
>ending times (option -b and -e).
>For most beginning and ending times this procedure works well, but for
>beginning times around 46000ps the routine 'g_order' gets stuck: I
>don't get an error message, but just the notice
>'Skipping frame 0time 45890.000' .
>Using later start times > 46100 works well again.
>I checked my .xtc file using several other routines, e.g. gmxcheck and
>trjconv to write a snapshot of the trajectory at the time im question,
>and it worked well.
>Does anybody know why this problem occurs and how it can be solved?
This is probably not specific for g_order. Does the trajectory have a
frame at 46000?
Could it be that the original framenumbers are still in place (i.e. step
Please run gmxdump on the xtc file and print the headers of the frames
at 46000 and the one before and after and send it to the list.
>Thanks for your help.
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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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