[gmx-developers] membed documentation

[Mark Abraham]

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> 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
>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20160317/36332c71/attachment.html>