Hi, I know this question has been asked for a few times already but I don't seem to get it. :( I did:
1) editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt dodecahedron 2) genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top 3) grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr and then I view the solv.gro file in VMD and found out that the protein is hanging out from the box as in the attached image: http://postimage.org/image/6df12u991/ I tried to put it in the centre with the command: 4) trjconv -s ions.tpr -f solv.gro -o solvcentre.gro -pbc mol -ur compact But it shows that the protein (solvcentre.gro) is still the same (hanging out from the box). Did I overlook something? Can I proceed with EM? Please advice. :( Thanking you in advance! Best regards -- View this message in context: http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
