[gmx-developers] membed documentation
erik.marklund at chem.ox.ac.uk
Thu Mar 17 18:17:38 CET 2016
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?
Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF
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