Does anyone know a command for separating pdb files after a simulation run in gromacs?

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Hamed Haghshenas

http://manual.gromacs.org/current/online/trjconv.html

Specially -sep option.

Best,

Nivedita Rai

Suppose you have run simulation for 5ns and save the trajectory for every 2fs and you want separate pdb at every 1ns than

trjconv -f md.xtc -s md.tpr -o protein.pdb -split 1000 -skip 500

hope it will work for you