version 3.3.3: trjconv -pbc mol
Created an attachment (id=275)
system in dodecahedron TIP5P water box
The system (in.gro) has a protein solvated in dodecahedron TIP5P water box. When using trjconv to visualize, the following options were tried and results shown:
trjconv -f in.gro -s in.gro -o out.pdb -pbc ? -ur compact
where ? is:
-mol: intact protein, part of protein sticking out of the box, box is rectagular
-whole: intact protein, part of protein sticking out of the box, box is rectagular
-atom: intact protein, dodecahedron, protein completely inside the box (this is what I am expecting)
According to Dr. David van der Spoel, The -mol option should in theory produce the same output as the -atom option.
#2 Updated by Rob Yang over 11 years ago
Created an attachment (id=276)
input (including *.itp, *.top, *.gro, *.mdp, and *.tpr)
input files that includes the tpr file. I had deleted the in.gro file submitted initially from my files. So I re-prepared the same system with all the other input files including tpr. Thank you.