[gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)
x.periole at rug.nl
Thu Feb 2 09:24:06 CET 2017
Indeed same Thomas has good points I could have mentioned.
Reduce the interface gap to a minimum of the system ca get stuck in stupid state … the two side should see each other, once they start merging it is fast.
> On 01 Feb 2017, at 20:01, Thomas Piggot <t.piggot at soton.ac.uk> wrote:
> I've actually used this suggested approach before (when making a larger membrane smaller). It can take a fair bit of simulation to equilibrate things at the periodic boundary, depending upon how you remove the lipids, how big you make the box at the boundary, etc. Not making the interface big enough, so as to try and make the gap between periodic images small for a quick equilibration, can easily lead to crashes due to overlapping atoms across the periodic boundary.
> What lipids and force field you are using will also massively impact the equilibration times. For a fast diffusing phospholipid (using a fast diffusing force field and cut-off settings), taking your original suggestion a), or the approach of Xavier may make the equilibration quick enough that it's not worth the effort of doing something more elaborate.
> On 01/02/17 17:30, Christopher Neale wrote:
>> Another great idea. Thanks Xavier! I'll report back on what I eventually do in a few weeks with info on issues and timescales necessary for relaxation so that it's available if anyone ever wants to do it in the future.
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of XAvier Periole <x.periole at rug.nl>
>> Sent: 01 February 2017 11:18:36
>> 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)
>> What about tilling 2x2 and then removing lipids that have x&y larger than a cutoff … then minimisation+equilibration of the interface even atomistic would be quite trivial.
>>> On 01 Feb 2017, at 17:14, Christopher Neale <chris.neale at alum.utoronto.ca> 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,
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> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
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