[gmx-users] elongated protein in production run
mark.j.abraham at gmail.com
Thu Apr 20 09:24:20 CEST 2017
This is entirely normal. Please see
On Thu, Apr 20, 2017 at 9:16 AM abhisek Mondal <abhisek.mndl at gmail.com>
> 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:
> 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.
> Abhisek Mondal
> *Senior Research Fellow*
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
> *Kolkata 700032*
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