Hi gmx users, I defined an octahedral box with this line:
$grxdir/editconf -f 1AKEallH.gro -o 1AKEallHbox.gro -bt octahedron -d 0.6 and then I solvated my protein with SPC water model: $grxdir/genbox -cp 1AKEallHbox.gro -p 1AKEallH.top -o 1AKEallHsol.gro -cs I am now watching the trajectory of an MD simulation with a molecular visualisation software (VMD) and I noticed 2 unexpected things: 1) part of the molecule is outside the box 2) the box is cubic Although the molecule is out of the box, the periodic boundary conditions should ensure a correct behaviour, still, why is it cubic? Note: after solvation, the system was neutralised with genion, then an EM steep, an EM cg and a all-bonds constrained MD were performed before the actual MD. Any ideas? Thanks, Stefano _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
