nahren manuel wrote:
Dear Gromacs Users,
I am performing a MD simulation of a dimer in a dodecahedron box. The
simulation stopped after 8 ns (power cut) and i had to restart to
complete it fully to 12 ns.
I then concatenated the two trajectories using trjcat
trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc
trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center
-boxcenter tric -o center.xtc
trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc
1. The above procedures does not center the molecule in the box.
The last operation fits to a structure, permitting rotations and
translations. If the target is not centered in its box...
2. The box seems to shift from one corner to the center. Especially for
the duration 8-12 ns (my restart run)
I feel I am missing something here. Kindly advice.
It's a periodic box - a mathematical construction. The simulation
doesn't care where the atoms go in relation to it. If you care, you can
apply trjconv afterwards.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
