On Oct 27, 2010, at 10:05 AM, leila karami wrote: > 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? Yes, I would try it that way. > > You said, (Then overlay both results in the visualization program). How? In pymol for example, just load both PDBs.
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