[gmx-users] how to create a proper box size for a membrane?

Ricardo O. S. Soares ross_usp at yahoo.com.br
Thu Feb 16 18:24:02 CET 2012

Hello Tsjerk,

Thanks for your reply!

I have take into account PBC for this system. In this case what procedure do I have to add it in the making of the membrane?
Is the best way to do it with one POPC residue and then multiplying into a bilayer with genconf or to download a  "membrane.pdb" and edit its size?
Don't know if its relevant here, but I intend to use Charmm27.

Thanks again,



> De: Tsjerk Wassenaar <tsjerkw at gmail.com>
>Para: Ricardo O. S. Soares <ross_usp at yahoo.com.br>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Enviadas: Quinta-feira, 16 de Fevereiro de 2012 15:08
>Assunto: Re: [gmx-users] how to create a proper box size for a membrane?
>Hi Ricardo,
>If you've generated your membrane without taking PBC into account,
>then I'd say measuring the extent and setting the box manually
>(editconf -box) is the best option you have.
>On Thu, Feb 16, 2012 at 5:44 PM, Ricardo O. S. Soares
><ross_usp at yahoo.com.br> wrote:
>> Hello dear users,
>> I'm familiar with solvated protein simulations for quite a while now.
>> Recently I'm beginning to study some membrane systems.
>> I have created a POPC membrane and now I need to make a proper box. Using
>> editconf, the box is always larger than the membrane's x and y  coordinates,
>> even controlling the -d option.
>> I could measure the membrane and set the box values manually, but that
>> doesn't seem to me to be a safe approach.
>> I read Justin Lemkul's tutorial on membranes, and I see that there were
>> already a box in the downloaded file, so I couldn't figure something out
>> from there yet.
>> Thanks
>> ---
>> Ricardo O. S. Soares , PhD Student.
>> Group of Biological Physics - Department of Physics & Chemistry
>> Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São
>> Paulo.
>> --
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>Tsjerk A. Wassenaar, Ph.D.
>post-doctoral researcher
>Molecular Dynamics Group
>* Groningen Institute for Biomolecular Research and Biotechnology
>* Zernike Institute for Advanced Materials
>University of Groningen
>The Netherlands
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