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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Feb 16 18:08:00 CET 2012

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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