From: Jie Shi (shijie0204_at_tamu.edu)
Date: Wed Sep 14 2022 - 11:00:34 CDT
A quick update: running simulation with just plain "useflexiblecell" still
lead to irregular membrane bending.... This is weird.
On Tue, Sep 13, 2022 at 12:03 AM Jie Shi <shijie0204_at_tamu.edu> wrote:
> Hi Norman,
>
> Thank you for your explanations! I will try this and hopefully, it will
> solve the problem (fingers crossed!)
> Thanks again!
>
> Best,
> Jie
>
>
> On Mon, Sep 12, 2022 at 11:40 PM Geist, Norman <
> norman.geist_at_uni-greifswald.de> wrote:
>
>> 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,
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>> 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 <
>> norman.geist_at_uni-greifswald.de> 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 <
>>> 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
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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!6SeLQhHJdsYeDGBxJU0yltodw8_sEAuwo5uUu8F5tbziPd65Oi6OOAVVfSEu5LuhTq4SeCv2Op2vvIeKNyGseVE$
>>>> <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
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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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