[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

David Mobley dmobley at gmail.com
Wed Mar 22 19:54:08 CET 2006


> My conclusion so far is that trr file must be used for rerun (we learn
> every day, isn't it fabulous !)
> and I do not see the bug you pointed out but probably due to the system
> I run !!

Well, that sounds like good news.

I am not surprised that the reduced precision trajectories give you
big energy differences with -rerun. LJ and bonded energies are very
sensitive to the distances between atoms.

It's possible the reason you didn't see the bug with 3.2 was that your
box size is the same for both of your tpr files and your original
trajectory, in which case this would cause no problems (the bug was
that mdrun failed to update the box sizes from the trajectory rather
than the tpr file, but if the box sizes are the same this would make
no difference).


> If you have more comment please ...
> Best wishes
> XAvier
> --
> ----------------------------------
> Xavier Periole - Ph.D.
> Dept. of Biophysical Chemistry / MD Group   Univ. of Groningen
> Nijenborgh 4
> 9747 AG Groningen
> The Netherlands
> Tel: +31-503634329
> Fax: +31-503634398
> email: x.periole at rug.nl
> web-page: http://md.chem.rug.nl/~periole
> ----------------------------------
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