[gmx-users] PBC issues with membrane-peptide simulation

[Abhi Acharya]

Dear users,

Well, I have found another solution for avoiding the diffusion through the
periodic boundary in such simulations. Hope this is helpful to others doing
similar work.

Basically, the idea is to apply a biasing potential to the COM of the
peptides to pull them towards the membrane so as to ensure interaction with
the lipid bilayer. Thereafter, normal production simulations can be
performed on the peptide membrane complex. See the following paper:

Li, J., Liu, S., Lakshminarayanan, R., Bai, Y., Pervushin, K., Verma, C.,
and Beuerman, R.W. (2013). Molecular simulations suggest how a branched
antimicrobial peptide perturbs a bacterial membrane and enhances
permeability. Biochim. Biophys. Acta *1828*, 1112–1121.

Best Regards,
Abhishek Acharya



On Thu, Nov 10, 2016 at 12:48 PM, Abhi Acharya <abhi117acharya at gmail.com>
wrote:

> Sorry for that Mark.
>
> Basically, our experimental studies show that our designed peptides (2-3
> different peptides)  are involved in membrane destabilization but their
> activity (in terms of MIC values) varies. We want to understand the
> molecular underpinnings of the membrane destabilization process and
> possibly explain the variation in activities of the peptides. Therefore, we
> wanted to perform some simulations starting from the point where some
> amount of peptides are randomly added to the simulation box on one side of
> the membrane (about 5 nm away from the upper leaflet) and see how the
> system evolves.
>
> The problem is that some of the peptides diffuse along the z-direction
> such that they exit the simulation box and appear on the other side near to
> the lower leaflet.
>
> Hope this is helpful.
>
> Thanks and Regards,
> Abhishek Acharya
>
>
>
>
>
> On Thu, Nov 10, 2016 at 9:57 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> You haven't said what you're trying to model, so it's going to be hard for
>> someone to help out :-)
>>
>> Mark
>>
>> On Thu, 10 Nov 2016 05:21 Abhi Acharya <abhi117acharya at gmail.com> wrote:
>>
>> > Thank you Stephane for your suggestion. Though this seems like a nice
>> > solution to circumvent the problem, but do you think this is the normal
>> way
>> > to go about it? I have never found anyone reporting such a methodology
>> for
>> > membrane peptide simulation. Also, I can anticipate significant
>> increase in
>> > computational costs for a double bilayer system. I have a 800 lipid
>> > molecules in a single bilayer, so this is significant factor for me.
>> >
>> > Thanks and Regards,
>> > Abhishek
>> >
>> > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 <
>> Stephane.ABEL at cea.fr
>> > >
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > it is not an issue !! To resolve your problem you could simulate two
>> > > bilayer in box and  insert the peptides between them.
>> > >
>> > > HTH
>> > >
>> > > ------------------------------
>> > >
>> > > Message: 6
>> > > Date: Wed, 9 Nov 2016 16:07:26 +0530
>> > > From: Abhi Acharya <abhi117acharya at gmail.com>
>> > > To: gromacs.org_gmx-users at maillist.sys.kth.se
>> > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
>> > > Message-ID:
>> > >         <CAB1aw3zkCH7wmR6Za9H4OHm1PLG95cAeO0HJksxyxZi8yXC9Cg at mail.
>> > > gmail.com>
>> > > Content-Type: text/plain; charset=UTF-8
>> > >
>> > > Dear Gromacs users,
>> > >
>> > > I am trying to simulate a system consisting of a lipid bilayer and few
>> > > peptides. The peptides have been added randomly to the simulation box
>> > only
>> > > on one side of the membrane. I ran a 100 ns simulation of the system
>> > using
>> > > CHARMM36 forcefeild. However, I find that within the first few ns,
>> some
>> > of
>> > > the peptides appear on the other side of the membrane. I think that
>> this
>> > is
>> > > because of the diffusion of the peptides though the periodic boundary.
>> > > Kindly suggest  how to tackle this problem. I have used COM motion
>> > removal
>> > > on the whole system for the said simulation.
>> > >
>> > > Regards,
>> > > Abhishek Acharya
>> > >
>> > >
>> > > ------------------------------
>> > >
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