I did simulation of protein-dna complex in water solvent. After
simulation, two strands of dna was separated when I displayed my a.xtc
with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc
nojump) and problem fixed. But now I have another problem. Before using
–pbc nojump, there were water molecules in interface of between protein
and dna but, After using of –pbc nojump, 1) there was no water molecule
in interface of between protein and dna. 2) The distance between water
molecules and protein or dna was increased.
I want to survey interfacial water molecules and dynamics of water
medited hydrogen bonds.
I had sent my question to gromacs mailing list, before, but my problem
was not solved.
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