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

[Abhi Acharya]

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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