[gmx-users] making bilayers including a lipid-like molecule

[Björn Sommer]

Dear Mohsen,

just use our MembraneEditor:

http://cm2.cellmicrocosmos.org

You can use your custom PDB files and import them into the 
MembraneEditor. You can use different packing algorithms, e.g. the 
Distributor, if you want to define the absolute number of lipids. Or use 
the Advanced Random Placing, if you just want to meet the percental 
distribution which you have defined. There are also some YouTube Videos 
on our WebPage.

The Java Webstart version usually runs without problems on Windows or 
Linux (e.g. Ubuntu or OpenSuse) - of course Java has to be installed!

New Macs are not supported yet, but I know already the solution for the 
problem and in the next version of the MembraneEditor it will also run 
on Mac again.

For vesicles, you can download the VesicleBuilder here:

http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=35&t=676

If you want to generate large vesicles, it is better to install the 
MembraneEditor on a local machine with Eclipse:

http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=18&t=697

But for medium membranes, such as 200x200 Angstrom, Java Webstart is 
sufficient.

It is version 1.11. If you have any problems, I am currently working on 
a version 1.12 and I will upload it soon. I can also send the actual jar 
file to you. For membrane and vesicle simulation, we also used GROMACS 
several times.

Special about the MembraneEditor is the support of rafts (so areas with 
different lipid compositions) and also multiple layers, e.g. for 
stacking or for the generation of multiple vesicles.

If you have any questions, just contact me.

Best wishes,
Björn

Am 16.04.2015 um 10:57 schrieb 
gromacs.org_gmx-users-request at maillist.sys.kth.se:
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>     1. making bilayers including a lipid-like molecule
>        (Mohsen Ramezanpour)
>     2. making bilayers including a lipid-like molecule
>        (Mohsen Ramezanpour)
>     3. Re: adding SR2++ to charm27 force field (Ming Tang)
>     4. minimum image convention (pratibha kapoor)
>     5. Re: Mdrun and minimum image convention
>        (Catarina A. Carvalheda dos Santos)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 15 Apr 2015 20:57:41 -0400
> From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>,
> 	Discussion list for GROMACS users
> 	<gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] making bilayers including a lipid-like molecule
> Message-ID:
> 	<CAERzrhu0BJuvgE3sO+zPgSXy=0DsaEGdTt97niYq5Q1Sghd23g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs users,
>
> I was wondering how can I make initial structures for bilayers, micells and
> liposomes composed of different lipids including some lipid-like molecules.
> I am interested in different mixing ratios in two leaflets in bilayer and
> liposome cases.
>
> I have the coordinate and topology files for these molecules.
>
> Looking at previous posts I found Membrane Builder, Membuilder II but I
> could not find any option for uploading my lipid-like molecules in those.
>
> Any tutorial for how to use Gromacs to build them?
>
> Any suggestion is appreciated in advance
>
> Cheers
> Mohsen
>
>
>