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

nd reply. regards nahren --- On *Wed, 4/22/09, Tsjerk Wassenaar //* wrote: From: Tsjerk Wassenaar Subject: Re: [gmx-users] -center -fit dodecahedron : dimer To: "Discussion list for GROMACS users" Date: Wednesday, April 22, 2009, 2:50 PM Hi Nahren, >

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

thanks for your attention and reply. regards nahren --- On Wed, 4/22/09, Tsjerk Wassenaar wrote: From: Tsjerk Wassenaar Subject: Re: [gmx-users] -center -fit dodecahedron : dimer To: "Discussion list for GROMACS users" Date: Wednesday, April 22, 2009, 2:50 PM Hi Nahren, > trjconv -f

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

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