[gmx-users] Regarding membrane construction

陈功 gchen511 at gmail.com
Mon Jun 9 09:22:55 CEST 2014

Dear Venkat,
I guess there are some other methods to generate  new lipid bilayer construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o new_conf.gro or using editconf & cat ...Another way, you can try the script packmol. Be more patient.  haha, I m also a new gmx user.
Good  luck,
chen gong

From: Venkat Reddy
Date: 2014-06-09 15:31
To: Discussion list for GROMACS users
Subject: [gmx-users] Regarding membrane construction
Dear all,
I am studying a membrane protein of length 288 residues. I want to simulate
in a DPPC bilayer. I have downloaded dppc equilibrated bilayer from Peter
Tieleman's website as directed by Justin in his membrane-protein tutorial.
But I found 128 lipid membrane is not enough for my protein. From the
literature, I found I need  81 lipids in each leaflet. How can I construct
a 162 lipid equilibrated bilayer? I tried CHARMM-GUI to build it. But the
equilibration is giving RATTLE error. Please help me in this regard.
Thank you
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 gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list