<p dir="ltr">Hi,</p>
<p dir="ltr">Doubtless there's room for improvement, but the relevant part of the user guide is at <a href="http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-a-membrane-protein-embedding-simulation">http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-a-membrane-protein-embedding-simulation</a></p>
<p dir="ltr">Mark </p>
<br><div class="gmail_quote"><div dir="ltr">On Thu, 17 Mar 2016 18:17 Erik Marklund <<a href="mailto:erik.marklund@chem.ox.ac.uk">erik.marklund@chem.ox.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Dear developers,
<div><br>
</div>
<div>I hope this is the right forum for this.</div>
<div><br>
</div>
<div>gmx mdrun -h gives the following information about -membed:</div>
<div><br>
</div>
<div>"The option -membed does what used to be g_membed, i.e. embed a protein into a<br>
membrane. This module requires a number of settings that are provided in a<br>
data file that is the argument of this option. For more details in membrane<br>
embedding, see the documentation in the user guide. The options -mn and -mp<br>
are used to provide the index and topology files used for the embedding.”</div>
<div><br>
</div>
<div>I am not sure what the ‘user guide’ refers to, but the manual provides no further information, a search at <a href="http://gromacs.org" target="_blank">gromacs.org</a> show nothing that is up to date, and <a href="http://manual.gromacs.org/programs/gmx-mdrun.html" target="_blank">http://manual.gromacs.org/programs/gmx-mdrun.html</a> 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.</div>
<div><br>
</div>
<div>It seems to me that the proper documentation for -membed is lacking, which we should address. Or am I missing something?</div>
<div><br>
</div>
<div>Kind regards,</div>
<div>Erik</div>
<br>
<br>
<div>
<div style="color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div>
<div>Erik Marklund, PhD</div>
<div>Postdoctoral Research Fellow, Fulford JRF</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
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