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 <abhi117acha...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
Message-ID:
<cab1aw3zkch7wmr6za9h4ohm1plg95caeo0hjksxyxzi8yxc...@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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