Omer Markovitch wrote:
Thanks.
I am not sure how this addresses my problem. I am getting "broken"
structure at the end of the MD (in confout.gro),
Well, you didn't say you were doing MD. I (and presumably Tsjerk)
thought you were converting your output from editconf. In such a case,
Tserk's suggestion lets you tile some boxes together to see how things
are (not) working. Your results will also depend on the contents of your
editconf -f file.gro. I suggest you copy and paste your actual commands
in future :-)
Mark
and want to be sure
that GMX treat it correctly during the MD.
To check your periodicity use genconf:
genconf -f in.pdb -o out.pdb -nbox 2 2 2
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