[gmx-developers] membed documentation

[Erik Marklund]

Hi Mark,

Thanks! Not so much of a developer question after all.

Kind regards,
Erik

On 17 Mar 2016, at 17:21, Mark Abraham <mark.j.abraham at gmail.com<mailto:mark.j.abraham at gmail.com>> wrote:


Hi,

Doubtless there's room for improvement, but the relevant part of the user guide is at http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-a-membrane-protein-embedding-simulation

Mark

On Thu, 17 Mar 2016 18:17 Erik Marklund <erik.marklund at chem.ox.ac.uk<mailto: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<http://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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