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: [email protected] <[email protected]> On Behalf Of RAHUL SURESH Sent: Tuesday, March 12, 2019 9:09 AM To: [email protected] 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 <[email protected]> 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: [email protected] > <[email protected]> On Behalf Of RAHUL > SURESH > Sent: Tuesday, March 12, 2019 6:23 AM > To: [email protected] > 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 * > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- *Regards,* *Rahul * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
