[gmx-users] elongated protein in production run
abhisek.mndl at gmail.com
Thu Apr 20 09:30:02 CEST 2017
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>
> This is entirely normal. Please see
> On Thu, Apr 20, 2017 at 9:16 AM abhisek Mondal <abhisek.mndl at gmail.com>
> > 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
> > 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
> > 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*
> > --
> > Gromacs Users mailing list
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
*Senior Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
More information about the gromacs.org_gmx-users