[gmx-users] problem facing after continuing the trajectory

[Rahul Karyappa]

Dear all,
    I have ran MD run on my system consisting of a polymer chain surrounded by ions and water molecules. First I ran MD run for total 3ns timesteps. We wanted to look at the radius of gyration behavior for the chains having different initial structures of the polymer chain. The initial Rg value of the chain was around 2nm and after 3ns MD simulation it was around 4-5 nm.
  What I did is I continued the trajectory for more 5ns. When I calculated the Rg value for the continued trajectory, the value for Rg at 3ns timestep was around 2nm. But at the end of the previous run (3ns) the value of Rg at 3ns timestep was around 4-5 nm. Why is it showing two different values of Rg for the same timestep?
Looking forward to your kind reply. Thanking you in advance.
Rahul Karyappa
NCL, Pune

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