[gmx-users] Continue finished job and Smoothing trajectories questions

David spoel at xray.bmc.uu.se
Wed Jun 15 09:06:08 CEST 2005

On Wed, 2005-06-15 at 09:53 +0300, itai bloch wrote:
> Hi all users,
> 1. When I have tried rerunning a finished job using my previous .trr
> file The .job file does not get updated. All the other output files
> .trr/.edr/.log are getting updated and the simulation seems to work
> fine except for the .job file?
gromacs doesn't write any .job files

> 2. Using g_filter with -ol on a PBC system resulted in a nice smoothed
> movement of all the multi-atoms molecules (e.g. protein and lipid) BUT
> the water (SOL) molecules are drifting away from the box? how can I
> keep it all in the box?
Use flag -jump
> I would appreciate your help or comments regarding these issues.
> Best regards, Itai.
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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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