Re: [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150

2011-02-21 Thread Tsjerk Wassenaar
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

Re: [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150

2011-02-21 Thread XAvier Periole
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

[gmx-users] Re: gmx-users Digest, Vol 82, Issue 150

2011-02-21 Thread Evelyne Deplazes
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