Dear Gromacs users and developers, I'm trying to visualize .trr from md simulation using VMD.
I see that starting from some point (probable as a result of a peptide drift ) my peptide splits and it seems like one part appears at one side of the box and the other on the opposite side. Both parts are connected with a very long bond. I want to center the peptide in the box and of course I want all the molecules to be wrapped accordingly. I checked the mailing list and I found that I can use trjconv (trjconv -f *.xtc -s *.tpr -o center.xtc -center -pbc nojump). I tried to use this command with .trr (trjconv -f *.trr -o center.trr -center -pbc) as a result the peptide is still not centered and all the water molecules diffuse out of my rectangular box. Am I doing something wrong? I'm trying to center the molecule not only for visualization but also because I want to analyze the simulation using VMD and scripts I made for analysis of NAMD simulations (I worked with NAMD for a long time and I need to work with gromacs because of SPCE water). Is it possible to perform analysis with VMD (I need commands like measure distance, measure angle, cut molecules at some radius from predefined residue and pbcwrap around some molecule or peptide)?
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