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:
>
>
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> ________________________________
> 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>_______________________________________________
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Received on Mon Jan 13 2020 - 07:00:03 PST
