[gmx-users] Pore size calculation

[pbuscemi at q.com]

If you actually can model water in the pore, then run a few experiments
changing the VDW radius of the water oxygen.  This will give you the
limiting size of the pore and this is the parameter you actually need to
know.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of RAHUL
SURESH
Sent: Tuesday, March 12, 2019 9:09 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Pore size calculation

Hi Mr. Paul.
It might not have been clear in my previous mail. Sorry for the
inconvenience.

I have simulated a GPCR membrane protein in POPC system. I need to calculate
the pore size in the protein structure and not in the lipid bilayer.
Precisely i am intended to calculate the water permeation through the
pathway in protein structure. So I want to measure the pore radius of the
protein structure and permeation of water through the pathway.

Thank you


On Tue, Mar 12, 2019 at 6:56 PM <pbuscemi at q.com> wrote:

> Rahul,
>
> What do you mean by pore size?  A hole in the membrane caused by 
> external tension ?  The space occupied by the protein ? Does lipid 
> occupy the walls of the pore ?
>
> Paul
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of RAHUL 
> SURESH
> Sent: Tuesday, March 12, 2019 6:23 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Pore size calculation
>
> Hi. I have a Protein_POPC bilayer system, simulated for 1000ns.
>
> Is it possible to calculate the pore size of the membrane protein?
> I tried a tool gmx_hole, but ended up with an unnotified error.
>
> Can anyone help me with this?
>
> Thanks in advance
> --
> *Regards,*
> *Rahul *
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--
*Regards,*
*Rahul *
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