Can anyone tell me the command for separating pdb files after a simulation is complete in gromacs?
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
http://manual.gromacs.org/current/online/trjconv.html
Specially -sep option.
Best,
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See above.
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