[AMBER] Fwd: Periodic box problem when simulating Membrane system

From: Tiejun Wei <t.wei.qmul.ac.uk>
Date: Mon, 13 Jan 2020 14:26:41 +0000

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


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Screenshot from 2020-01-13 13-23-32.png
(image/png attachment: Screenshot_from_2020-01-13_13-23-32.png)

Screenshot from 2020-01-13 13-23-26.png
(image/png attachment: Screenshot_from_2020-01-13_13-23-26.png)

Received on Mon Jan 13 2020 - 06:30:03 PST
Custom Search