It looks the same as you have shown, you just have to image it during
trajectory analysis (autoimage) but before using rmsd analysis flag. Hope
you have used periodic boundary condition.
Thanks
// Zahoor
On Mon 13 Jan, 2020, 8:14 PM Gustaf Olsson, <gustaf.olsson.lnu.se> wrote:
> Assuming you are using periodic boundary conditions, are you “wrapping”
> you system back to the original volume? What does your MD input file look
> like.
>
> Best regards
> // Gustaf
>
>
> > On 13 Jan 2020, at 15:26, Tiejun Wei <t.wei.qmul.ac.uk> wrote:
> >
> >
> >
> > Get Outlook for Android<https://aka.ms/ghei36>
> > ________________________________
> > From: Tiejun Wei <t.wei.qmul.ac.uk>
> > Sent: Monday, January 13, 2020 1:30:24 PM
> > To: amber.ambermd.org <amber.ambermd.org>
> > Subject: Fw: Periodic box problem when simulating Membrane system
> >
> >
> >
> >
> > Tiejun Wei
> >
> > <http://www.qmul.ac.uk/lifesciences/research/phd/index.html>CSC<
> http://www.sbcs.qmul.ac.uk/postgraduate/research/studentships/china-scholarship-council/>
> PhD student
> >
> > Computational Biology/Biophysics
> >
> > <https://bessantlab.org/>DuffyLab<http://www.duffylab.co.uk/> (QMUL)
> > [http://www.daviddang.uk/icon/linkedin-sig.png]<
> https://www.linkedin.com/in/tiejunwei/>
> >
> > ________________________________
> > From: Tiejun Wei
> > Sent: Monday, January 13, 2020 1:28 PM
> > To: amber.ambermd.org <amber.ambermd.org>
> > Subject: Periodic box problem when simulating Membrane system
> >
> > Hi AMBER users:
> >
> > I'm using AMBER to simulate a membrane system and found my TIP3P water
> molecules are "spreading". (see pics attached)
> >
> >
> > The system was generated by CHARMM-GUI but I'm not using auto-generated
> constraint files.
> >
> > I'm not particularly interested in protein structural change, we focus
> more on the co-factors of the protein. Just curious, is this normal?
> >
> > If not, what's the correct scenario looks like? is there any examples of
> AMBER/NAMD config files for membrane simulation?
> >
> > Best,
> > Tiejun
> > <Screenshot from 2020-01-13 13-23-32.png><Screenshot from 2020-01-13
> 13-23-26.png>_______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jan 13 2020 - 07:30:02 PST
