From: Jie Shi (shijie0204_at_tamu.edu)
Date: Tue Sep 13 2022 - 00:28:30 CDT
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 <
norman.geist_at_uni-greifswald.de> 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
> ZjQcmQRYFpfptBannerStart
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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!_zclHGZ856CoWXbpk3T-4csxD18kwTNzCZghDMxw9IEtaxQJp4YEknkBOqGbIeLwENK3Z_w-UdwGNkDam8VSWl8$
> <https://urldefense.com/v3/__https://postimg.cc/jWrpgPFH__;!!DZ3fjg!8SGM2Y0Iiu5eCxBnsVlOZz8ct9MyjB_EKDU41jkwZp3ebOuLMORPoAO47xBkkAO36ib1bihdLbpiEmoIszuz18cuB8iBjg$>
>
>
> 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
>> ZjQcmQRYFpfptBannerStart
>> This Message Is From an External Sender
>> This message came from outside your organization.
>>
>> ZjQcmQRYFpfptBannerEnd
>>
>> 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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