[gmx-users] Pore size calculation

[RAHUL SURESH]

Thank you for your answer but still I am unclear.
During the simulation there is water molecules which pass through the pore.
Can you kindly explain the second part about changing the vdw radii? Sorry
for the inconvenience.


On Tue 12 Mar, 2019, 8:16 PM , <pbuscemi at q.com> wrote:

> 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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