Hi,

This is entirely normal. Please see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Thu, Apr 20, 2017 at 9:16 AM abhisek Mondal <abhisek.m...@gmail.com>
wrote:

> Hi,
>
> I'm trying to simulate a protein for 40ns after 20ns nvt and 20ns npt
> equilibration, respectively. After nvt and npt equilibration steps the
> protein looks fine to me. But when I analyze the trajectory file generated
> after 40ns of production run, I found some unusual facts.
> Half of the trajectory seems fine, then suddenly the loops and sheets of
> the protein got elongated and after some time it came back to normal.
>
> Can you please tell me is there any mistake I'm making during simulation ?
> I have kept a screenshot of elongated-protein (trajectory snapshot) in the
> following link:
> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>
> The backbone RMSD (after production run) seems to fluctuate at the
> beginning but reached some stable value after sometime and so does the
> radius of gyration.
>
> Please suggest me a way out.
>
> Thanks
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
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