Thank you for your email.
I also have not observed such a phenomenon either.
I appreciate you bringing this to my attention.
Best regards
Jinyoung.
2024년 6월 25일 (화) 오전 7:51, Dickson, Callum <callum.dickson.novartis.com>님이
작성:
> Hi, I would tend to monitor the X- and Y- dimensions over the TI windows.
> I would be surprised if you see a dramatic change in short runs.
>
>
>
> I do not have familiarity with using ntp=4, so I can’t comment on this
> setting.
>
>
>
> Best,
>
> Callum
>
>
>
>
>
> *From:* 변진영 / 학생 / 약학과 <byunjy0614.snu.ac.kr>
> *Sent:* Saturday, June 22, 2024 10:14 AM
> *To:* Dickson, Callum <callum.dickson.novartis.com>
> *Cc:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] Using ntp=1 for membrane embedded Protein-Ligand
> System with ifsc=1 Option
>
>
>
> Hi Callum, Thank you for your detailed response and the helpful workflow
> suggestion. I have a couple of follow-up questions based on your advice:
> You mentioned that running membrane proteins under ntp=1 for hundreds of
> nanoseconds may cause
>
> ZjQcmQRYFpfptBannerStart
>
> *This Message Is From an Untrusted Sender *
>
> You have not previously corresponded with this sender.
>
> ZjQcmQRYFpfptBannerEnd
>
> Hi Callum,
>
> Thank you for your detailed response and the helpful workflow suggestion.
>
> I have a couple of follow-up questions based on your advice:
>
> You mentioned that running membrane proteins under ntp=1 for hundreds of
> nanoseconds may cause membrane contraction along either the X- or Y-axis.
> If I observe significant changes in the membrane during short TI windows,
> what steps should I take to mitigate this issue?
>
> Would it be possible to use ntp=4 intermittently during the data
> collection RBFE simulation to adjust the box size with protein-ligand
> positional restraint (not for data collection later)?
> If so, how frequently would you recommend doing this?
>
> Thank you again for your guidance.
>
> Best regards,
> Jinyoung
>
>
>
> 2024년 6월 19일 (수) 오후 1:10, 변진영 / 학생 / 약학과 <byunjy0614.snu.ac.kr>님이 작성:
>
> Hi Callum,
>
> Thank you for your detailed response and the helpful workflow suggestion.
>
> I have a couple of follow-up questions based on your advice:
>
> You mentioned that running membrane proteins under ntp=1 for hundreds of
> nanoseconds may cause membrane contraction along either the X- or Y-axis.
> If I observe significant changes in the membrane during short TI windows,
> what steps should I take to mitigate this issue?
>
> Would it be possible to use ntp=4 intermittently during the data
> collection RBFE simulation to adjust the box size with protein-ligand
> positional restraint (not for data collection later)?
> If so, how frequently would you recommend doing this?
>
> Thank you again for your guidance.
>
> Best regards,
> Jinyoung
>
>
>
> 2024년 6월 18일 (화) 오전 12:56, Dickson, Callum <callum.dickson.novartis.com>님이
> 작성:
>
> Hi, this came up recently on the mailing list. Here was my response-
>
> My typical workflow for free energy on membrane proteins with TI would be
> ? Equilibrate the system (receptor+single ligand) under NPT with
> semiisotropic barostat (ntp=3) for >100 ns
> ? Prepare/dock remaining ligand set using the equilibrated system
> ? Run TI windows using ntp=1. Although it would be preferable to
> keep ntp=3, this is not currently possible and since TI windows are
> typically short (on the order of 5 ns) you should not expect large changes
> in the membrane during these windows
>
> If you run membrane proteins under ntp=1 for hundreds of nanoseconds, you
> may see the membrane contracting along either the X- or Y- axis (such that
> it thins in one dimension and expands in the other). This is the motivation
> for the semiisotropic barostat, but short 5-10 ns TI windows are unlikely
> to encounter this.
>
> Best,
> Callum
>
>
> -----Original Message-----
> From: 변진영 / 학생 / 약학과 via AMBER <amber.ambermd.org>
> Sent: Monday, June 17, 2024 6:11 AM
> To: amber.ambermd.org
> Subject: [AMBER] Using ntp=1 for membrane embedded Protein-Ligand System
> with ifsc=1 Option
>
> !-------------------------------------------------------------------|
> This Message Is From an External Sender
> This message came from outside your organization.
> |-------------------------------------------------------------------!
>
> Dear AMBER Community,
>
> I am currently working on a simulation involving a membrane-embedded
> protein-ligand system. Typically, for such systems, I used the following
> settings:
> - barostat = 2
> - ntp = 3
> - csurften = 3
> - gamma_ten = 0.0
> - ninterface = 2
>
> However, I have encountered an issue when trying to calculate the relative
> binding free energy of the protein-ligand system using the '*ifsc*' option.
> The 'ifsc' option only supports ntp=1, which conflicts with my usual
> settings for membrane-embedded systems.
>
> Given this constraint, I am seeking advice on whether it is acceptable to
> run the simulation with ntp=1 for a membrane-embedded protein-ligand system.
> Are there any potential issues or considerations I should be aware of when
> using this setting?
>
> Any insights or recommendations from those with experience in similar
> simulations would be greatly appreciated.
>
> Thank you for your assistance.
>
> Best regards,
>
> Jinyoung
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Received on Sun Jun 30 2024 - 10:30:01 PDT
