Hi Chris,
Thank you so much for your suggestions!
I did not fully understand your "option 1" method, you mean use a nmr type restraint(nmropt=1) of distance between the molecules and the COM along the bilayer or some central selection in my channel protein? If yes, then my oiginal purpose is to use the concentration gradient effect to help my subsrate molecules to pass through the protein channel (maybe also need other external conditions such as external electric fields), so is this method still applicable? And you said "add a pretty good sized buffer", could you give me more detailed information about it?
All the best,
Wu Meng
------------------------------
Message: 4
Date: Mon, 5 Jun 2017 21:29:05 -0600
From: Chris Neale <candrewn.gmail.com<mailto:candrewn.gmail.com>>
Subject: Re: [AMBER] set substrate concentration gradient difference
acorss membrane
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
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option 1) use a separate flat-bottomed restaining potential on each ion,
perhaps controlling its distance from the membrane center of mass along the
bilayer normal or along the Z dimension away from some central selection in
your channel protein. Use a non-penalized width that permits ions to be
above and below the channel/bilayer but never so far away that they can
wrap around PBC (check that this is true even for the smallest Z that you
could get with volume fluctuations if doing constant pressure). Personally,
I'd add a pretty good sized buffer to be sure that this was always true.
option 2) build a unit cell with two membranes, each with one channel and
have the extracellular end of each channel face a central aqueous resevoir
with ions but don't put any ions in the other system. This actaully isn't
so bad since even though the system gets a lot bigger and therefore slower,
you have an intrinsic repeat with multiple channels per simulation system.
option 3) don't use PBC
option 4) embed your channel in a small vessicle where there is an
inherrent inside vs. outside
I'm sure there are other options, and some will be better than others
depending on your goals.
On Mon, Jun 5, 2017 at 7:07 PM, Meng Wu <wumeng.shanghaitech.edu.cn<mailto:wumeng.shanghaitech.edu.cn>> wrote:
>
> Dear All,
>
> Forgive me to send this message again and I really need some advice to
> go on my work.
>
> I am studying a channel protein and I want to set a substrate
> concentration gradient difference acorss membrane in the MD simulation
> process to see if the concentration gradient difference could push the
> substrate molecule pass through the channel or not. But it's hard to keep
> the gradient difference due to periodic boundary conditions without other
> special treatments. Is there any way to set the gradient difference acorss
> membrane?
>
> Any suggestions would be greatly appreciated.
> Thank you in advance!
>
> All the best,
> Wu Meng
> _______________________________________________
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> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
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>
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Received on Thu Jun 08 2017 - 19:30:02 PDT
