Hi Carsten
Thanks for your answer. You got my case very well. I understand your mean as follows: 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group =protein-dna) Is that true? You said, (Then overlay both results in the visualization program). How?
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