Hi, I try to remove the periodicity
You don't remove periodicity. -pbc nojump removes jumps due to (over) the PBC, not the PBC itself. to get a new .xtc file and one .gro > file. The commands are shown below: > "trjconv -f original.xtc -s original.tpr -n index -o frame_0.gro -dump 0 > -pbc nojump" Since your frame_0 will hold the same coordinates as your .tpr file, -pbc nojump serves no purpose here. "trjconv -f original.xtc -s original.tpr -n index -o new.xtc -pbc > nojump" > When I use g_rms to calculate the rmsd by new .xtc and .gro file, there > is a warning and other things goes well. Command i used is "g_rms -f > new.xtc -s frame_0.gro -o rmsd.xvg" and the warning is "can not make > broken molecules whole without a run input file,don't worry, mdrun > doesn't write broken molecules". I think i have removed the boundary, > and why it says there is an broken protein? It doesn't say there's a broken molecule. It says it couldn't fix one if it were present, because you don't provide topology information. But it also says that an .xtc file generated by mdrun (and not otherwise processed) doesn't contain broken molecules. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
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