[gmx-developers] membed documentation

Mark Abraham mark.j.abraham at gmail.com
Thu Mar 17 18:21:31 CET 2016


Doubtless there's room for improvement, but the relevant part of the user
guide is at


On Thu, 17 Mar 2016 18:17 Erik Marklund <erik.marklund at chem.ox.ac.uk> wrote:

> Dear developers,
> I hope this is the right forum for this.
> gmx mdrun -h gives the following information about -membed:
> "The option -membed does what used to be g_membed, i.e. embed a protein
> into a
> membrane. This module requires a number of settings that are provided in a
> data file that is the argument of this option. For more details in membrane
> embedding, see the documentation in the user guide. The options -mn and -mp
> are used to provide the index and topology files used for the embedding.”
> I am not sure what the ‘user guide’ refers to, but the manual provides no
> further information, a search at gromacs.org show nothing that is up to
> date, and http://manual.gromacs.org/programs/gmx-mdrun.html only states
> that "The option -membed does what used to be g_membed, i.e. embed a
> protein into a membrane. The data file should contain the options that
> where passed to g_membed before. The -mn and -mp both apply to this
> as well.” That is, it refers to the 4.5.X docs.
> It seems to me that the proper documentation for -membed is lacking, which
> we should address. Or am I missing something?
> Kind regards,
> Erik
> Erik Marklund, PhD
> Postdoctoral Research Fellow, Fulford JRF
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