[gmx-users] the treatments of the periodic boundary condition

[15110700076 at fudan.edu.cn]

Hello everyone,
      My several systems of  a protein-ligand complex were put into the dodecahedron box and were applied to 20ns runs. However, the ligands in these systems ran out of the boxes in the raw trajectories. After I treated these trajectories by "trjconv", the ligands and proteins could not come into the box at the same time. But the ligands were closed to the holes in waters where the proteins should be, it suggests that ligands should form H-bonds with proteins in some time points. How can I do to get the whole complex in the box, or the ligands may be distant from proteins in truth. My trajectory treatment commands are following:
trjconv -f md_0-20ns.xtc  -s md_1.tpr -o md_0-20ns_nojump.xtc -pbc nojump -n system.ndx
trjconv -f md_0-20ns_nojump.xtc -s md_1.tpr -o md_0-20ns_nojump_fit.xtc -fit rot+trans -n system.ndx
trjconv -f md_0-20ns_nojump_fit.xtc -s md_1.tpr -o md_every100ps.pdb -dt 100 -n system.ndx


thank you!



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Best wishes, 

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Qing Liu

Fudan Univ.

E-mail: 15110700076 at fudan.edu.cn