[gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

Christopher Neale chris.neale at alum.utoronto.ca
Wed Feb 1 17:47:19 CET 2017


I knew somebody smarter than me could come up with a better idea. Thanks Tom, your full embedding idea sounds like a fantastic way to go.

Thank you,
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Thomas Piggot <t.piggot at soton.ac.uk>
Sent: 01 February 2017 11:29:52
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

I've never done it, but for what it's worth of your two options b) would
be the way I would go. Equilibration of the system in a) could take
quite a long amount of time which you can save some of by doing this at
the CG level. Once you convert back to atomistic, you will probably also
need to run some further equilibration with restrains but I imagine for
far less time than in option a).

The only other thing that springs to mind which you could do would be to
take your complete membrane/protein system and insert that whole thing
into a larger membrane. So, in effect, treat your current membrane and
protein as you would do with just a protein that you wanted to insert
into an existing membrane. Given these tools are generally designed to
disturb the membrane system as little as possible, if you can get this
to work, you should end up with a system that isn't too disturbed at the
boundary of old and new lipids.



On 01/02/17 16:14, Christopher Neale wrote:
> Dear Users:
> I have some atomistic systems of a membrane protein embedded in a lipid bilayer. I currently have N lipids and I would like to increase that to 1.5N or 2N lipids (distributed equally in the bilayer plane) without disturbing the existing structure. Increasing to 4N lipids would be relatively easy by tiling the exisintg lipids 2x2 in XY. I am writing to ask if anybody has ever done this and if they have any suggestions.
> The ideas that I have at present are:
> a) add lipids and equilibrate (using restaints on existing lipids and protein). Increase in size could be by simply increasing XY dimensions and then using gmx genbox, knowing that I will end up with a bilayer defect at the edges that I will have to heal by MD.
> b) convert to a CG model, add lipids and equilibrate, then back to an AA model (using restaints on existing lipids and protein)
> I realize it sounds like an absurd requirement, but for scientific reasons in this particular case I can not simply start over by embedding the protein in a new, larger bilayer (i.e., it’s not just about saving compute time when generating the larger systems).
> Thank you for any advice,
> Chris.

Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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