From: Geist, Norman (norman.geist_at_uni-greifswald.de)
Date: Tue Sep 13 2022 - 01:40:34 CDT
Using "useconstantarea" will cause the box to only change in the
Z-dimension, useful to only equilibrate the solvent above and below a
surface with fixed bulk properties. Using "useconstantratio" will keep
the ratio between X and Y constant, also useful wich e.g. a crystal
surface. In your case, you may just plain want "useflexiblecell" with
none of the above, so each dimension can relax on its own.
Bests
Norman Geist
Am Dienstag, den 13-09-2022 um 07:36 schrieb Jie Shi:
I tried "useflexiblecell" along with "useConstantArea" (replacing the
constant ratio). But no, I have not tried just using "useflexiblecell"
without "useConstantArea" or "useconstantratio".
This idea is new to me. Do you think this may be the cause?
Best,
Jie
On Mon, Sep 12, 2022 at 10:31 PM Geist, Norman wrote:
Have you tried without useconstantratio? Am Dienstag, den 13-09-2022
um 07: 28 schrieb Jie Shi: Hi Norman, Thanks for the clarification.
Yes, I did have both "useflexiblecell" and "useconstantratio" set on
in my input configuration files, but
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Have you tried without useconstantratio?
Am Dienstag, den 13-09-2022 um 07:28 schrieb Jie Shi:
Hi Norman,
Thanks for the clarification. Yes, I did have both "useflexiblecell"
and "useconstantratio" set on in my input configuration files, but
still, I got no luck. The membrane bending is still there...
Best,
Jie
On Mon, Sep 12, 2022 at 10:22 PM Geist, Norman wrote:
I'd go with an NPT equilibration step that includes "useflexiblecell"
to allow each dimension to relax independently. The lipids just ask
for more room in one dimension, which cannot be resolved with
"useconstantratio". Bests
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I'd go with an NPT equilibration step that includes "useflexiblecell"
to allow each dimension to relax independently. The lipids just ask
for more room in one dimension, which cannot be resolved with
"useconstantratio".
Bests
Norman Geist
Am Dienstag, den 13-09-2022 um 00:17 schrieb Jie Shi:
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!7I1uDSlTHf8_mcUNyOi8cct4280iUxUMnIiUHP074KmJ1IOG14BDXA44ihvBAuGqOCHcwQp0yXz1W80TAEKByABM_4vSvcATGQ$ [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.
* 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.
* 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 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 on behalf of namd-l digest Sent:
Monday, September 12, 2022 1:06:19 PM To: 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 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
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
Links:
------
[1]
https://urldefense.com/v3/__https://postimg.cc/jWrpgPFH__;!!DZ3fjg!8SGM2Y0Iiu5eCxBnsVlOZz8ct9MyjB_EKDU41jkwZp3ebOuLMORPoAO47xBkkAO36ib1bihdLbpiEmoIszuz18cuB8iBjg$
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