[gmx-users] Setting up a complex membrane simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Nov 2 17:52:28 CET 2012

Hi Jonas,

Do you mean atomistic or coarse grained? Of course you should mean coarse
grained as it's out of the question to reach equilibration for a
significant amount of lipids with such complexity, which will take several
microseconds. I have a tool for building membranes, which could be of
value. You can contact me off list if you want.



On Fri, Nov 2, 2012 at 4:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 11/2/12 11:15 AM, jonas87 wrote:
>> Dear all,
>> I wish to run a simulation of a membrane consisting of about 10 different
>> lipids.
>> Through the automated topology builder ( example
>> <http://compbio.biosci.uq.edu.**au/atb/download.py?molid=1556<http://compbio.biosci.uq.edu.au/atb/download.py?molid=1556>>
>>  ) I can obtain
>> of each lipid a structure file in pdb format (it has one single molecule)
>> and an .itp topology file.
>> I want to make a random mix of these lipids with water and let it
>> equilibrate over 300 us or so to let it assemble into a bilayer.
>> My question is, how can I combine all these structures and topologies into
>> one system that has X molecules of lipid A, Y molecules of lipid B, etc. I
>> think genbox might have the answer for combining the sructures, but how?
> Building lipid membranes is complicated.  In theory, you could position
> individual molecules in specific orientations within a given box with
> editconf to form patches that can then be translated and rotated in any way
> you desire, or replicated with genconf -nbox.  I have only ever done this
> for a single-component lipid membranes.
> The topology is actually easier.  After #including the parent force field,
> you simply #include each lipid topology individually.  The [molecules]
> section then must reflect the contents of the coordinate file with respect
> to the number of molecules and the order they appear.
>  Also, if someone could point me towards a tutorial were they let a
>> membrane
>> form from a random distribution of a lipid with water that would be
>> useful.
>> The only GROMACS membrane tutorials that I can find always start with
>> pre-equilibrated membranes of 128 DOPC molecules.
> To my knowledge, there is no such tutorial (if it's not on the Tutorials
> page or found via Google, it doesn't exist).  You can randomly insert
> molecules into a box with genbox -ci -nmol and then fill with solvent later.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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