[gmx-users] Protein coming out of simulation box.

zaved at tezu.ernet.in zaved at tezu.ernet.in
Thu Aug 3 10:25:42 CEST 2017


I had performed a 100ns protein simulation with gromacs 5.1.4.

After the simulation I observed that the protein is coming out of the box.

I have used the following commands to correct it:

gmx_mpi trjconv -f md.xtc -s md.tpr -pbc mol -ur compact -center -o out.xtc

gmx_mpi trjconv -f out.xtc -s md.tpr -dt 100 -o file.pdb

Part of the protein is still out of the box (in the file.pdb).

Please suggest.

Thank You

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