[gmx-users] -pbc nojump

leila karami karami.leila1 at gmail.com
Wed Oct 20 12:07:11 CEST 2010

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
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