From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Mon Sep 12 2022 - 03:55:06 CDT
Hi Jie,
I am unable to download the attachment so there's a bit of guess work here.
1. Large membrane patches (>5-10 nm side) show membrane undulations. These are ripple like movements/bending. Is the curvature you are looking at is static or moves up-down/back-forth?
2. If these are undulations, you easily suppress these by restraining some of the atoms (e.g. phosphate groups of a few lipid molecules). Just apply restraints in the z-direction so the bulges don't form but lipids can diffuse within the membrane (x-y direction).
3. In membranes, it is common to use semi-isotropic pressure coupling. Are you using isotropic coupling?
For membranes, i have worked on Gromacs but some of these principles are applicable to all MD programs.
Regards,
Raman
________________________________
From: owner-namd-l-digest_at_ks.uiuc.edu <owner-namd-l-digest_at_ks.uiuc.edu> on behalf of namd-l digest <owner-namd-l-digest_at_ks.uiuc.edu>
Sent: Monday, September 12, 2022 1:06:19 PM
To: namd-l-digest_at_ks.uiuc.edu <namd-l-digest_at_ks.uiuc.edu>
Subject: namd-l digest V1 #3281
namd-l digest Monday, September 12 2022 Volume 01 : Number 3281
In this issue:
Re: namd-l: Fwd: Irregular spontaneous membrane bending even in the absence of protein
Re: namd-l: Fwd: Irregular spontaneous membrane bending even in the absence of protein
Re: namd-l: QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation.
----------------------------------------------------------------------
Date: Sun, 11 Sep 2022 15:38:29 -0500
From: Jeff Comer <jeffcomer_at_gmail.com>
Subject: Re: namd-l: Fwd: Irregular spontaneous membrane bending even in the absence of protein
It looks to me like you are doing everything right. Ibve run a lot of
membrane simulations based on CHARMM-GUI structures and have never seen
anything similar. How long does it take the curvature to appear? Have you
tried running longer to see if the curvature disappears?
Jeff
On Sun, Sep 11, 2022 at 10:42 Jie Shi <shijie0204_at_tamu.edu> wrote:
> Dear all,
>
> I am attempting to run a simulation of a system containing both membrane
> (POPC) and protein with NAMD 2.14 on HPC. However, I found the membrane
> forms an irregular spontaneous bending. So I then tested it with a
> membrane-only system (without the protein, so only the POPC bilayer, water,
> and ions are included), and a similar bending is again shown up, which
> suggests itbs not the protein that induces the bending in the membrane--_000_PN3PR01MB609587926603C3CB70113E53B3449PN3PR01MB6095INDP_--
This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST