From: Jie Shi (shijie0204_at_tamu.edu)
Date: Mon Sep 12 2022 - 17:17:12 CDT
Hi Raman,
Thank you for your reply. The snapshot showing the membrane bending can be
found here: https://urldefense.com/v3/__https://postimg.cc/jWrpgPFH__;!!DZ3fjg!4KeCsbvCamnUePtZAGRhbV8d_AMwIFtg8_szZCjRcRU2HY-NySRi5LogZps_fZeh6f4d03odtg840PKXairwLVo$
1. Large membrane patches (>5-10 nm side) show membrane undulations.
These are ripple-like movements/bending. Is the curvature you are looking
at static or moves up-down/back-forth?
Once the curvature is formed, it became quite stable and does not move
much. It’s as if the bent form is the stabilized form for the membrane
structure.
1. 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).
Yes, but our ultimate goal of the simulation is to study how the protein
would affect the membrane, especially the potential capability of
membrane-bending. For that purpose, we can not apply restraints as it will
also prohibit the membrane change we would like to study.
1. In membranes, it is common to use semi-isotropic pressure coupling.
Are you using isotropic coupling?
We use constant P and T along with “useConstantRatio yes”, is this the
semi-isotropic pressure coupling that you were referring to?
Best,
Jie
On Mon, Sep 12, 2022 at 2:11 AM Raman Preet Singh <
ramanpreetsingh_at_hotmail.com> wrote:
> 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
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> 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. Ib ve 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 itb s not the protein that induces the bending in the membrane
>
>
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