Hi Evelyne,
> 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc
The option -pbc mol IIRC relates to the option for the unit cell
representation (-ur). To unbreak molecules using trjconv, you need to
have .tpr file and use the option -pbc whole.
> 2) trjconv -f trajout_m
ok this does not make sense! Did you check your tpr file?
the command 1) should give you a trajectory where the molecules
are whole but jumping across the boundaries ... if it does not that
means that the tpr is fucky!
Try to visualize your tpr in vmd ... night give you some insight on
what is
I tried a couple of things according to your suggestions, but no luck so far
I used the following commands
1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc
2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc
no luck...If I use command 1) only the
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