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

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Wed Nov 9 12:23:04 CET 2016


it is not an issue !! To resolve your problem you could simulate two bilayer in box and  insert the peptides between them. 



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
        <CAB1aw3zkCH7wmR6Za9H4OHm1PLG95cAeO0HJksxyxZi8yXC9Cg at mail.gmail.com>
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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.

Abhishek Acharya


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