[gmx-users] peptide out of box

[Rakesh Mishra]

When I run simulations on a 42 residue peptide with a box size of 2.2 nm , I
find that after 4 ns , the peptide comes out of the box . Is this a problem
as far as the accuracy of the simulation results are concerned. Do the
periodic conditions account for such cases? If not , is there any suggestion
as to how I may salvage my data without having to start all  over again .

Cheers

Rakesh

Bachelors Student
Anna University
India
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