[gmx-users] elongated protein in production run

[abhisek Mondal]

Hello Mark,

Alright. However, building on previous .cpt I have extended my production
run for 10 more ns.

Thanks for you time. Much appreciated.

On Thu, Apr 20, 2017 at 12:54 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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.mndl at 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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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*