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

[Mark Abraham]

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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