Hi gromacs users
I study simulation of protein-dna interaction using gromacs. After full md simulation, because of diffusion of one strand of dna to edge of box, I used trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur compact –center. By this way my first problem is solved. 1) Should I use new xtc file for analysis section? 2) When I see new xtc file, there isn’t any water molecule in interface between protein and dna(where as there were water molecules interface between protein and dna, before full md simulation). I want to survey water mediated hydrogen bond between protein and dna. Do –pbc nojump cause to this problem?
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