[gmx-users] -center -fit dodecahedron : dimer

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

Re: [gmx-users] -center -fit dodecahedron : dimer

Hi Nahren, 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.

Re: [gmx-users] -center -fit dodecahedron : dimer

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

Re: [gmx-users] -center -fit dodecahedron : dimer

and reply. regards nahren --- On Wed, 4/22/09, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] -center -fit dodecahedron : dimer To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, April 22, 2009, 2:50 PM Hi

Re: [gmx-users] -center -fit dodecahedron : dimer

--- On *Wed, 4/22/09, Tsjerk Wassenaar /tsje...@gmail.com/* wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] -center -fit dodecahedron : dimer To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, April 22, 2009, 2:50 PM Hi Nahren