[gmx-users] gromacs 5.0

[Reid Van Lehn]

I haven't used membed with v5.0, but in v4.6.5 you make a text file with
the options that you can still find in the legacy g_membed help
documentation: http://manual.gromacs.org/online/g_membed.html

e.g. a file with something like:

nxy                      = 1000
nz                       = 0
xyinit                   = 0.150000
xyend                    = 1.000000
zinit                    = 1.000000
zend                     = 1.000000
rad                      = 0.220000
ndiff                    = 0
maxwarn                  = 0
pieces                   = 1
asymmetry                = no

Then pass this file to mdrun with the -membed option (after making an
appropriate membed.mdp file, using grompp, etc.). I also recommend checking
the appendix of the g_membed paper if you haven't read it yet for some more
details on what the different options do. They have a sample mdp file as
well - http://wwwuser.gwdg.de/~ggroenh/membed.html.

Reid


On Tue, May 6, 2014 at 9:54 AM, Anders Gabrielsson <andgab at kth.se> wrote:

> As far as I can tell, it is not documented what should go into this file
> other than "The data file should contain the options that where passed to
> g_membed before." from mdrun help text.
> I guess the documentation for the specific mdp settings also went out with
> the g_membed binary? (both man page and pdf manual entry)
>
> /Anders
>
>
> On 30 Apr 2014, at 09:35, Carsten Kutzner <ckutzne at gwdg.de<mailto:
> ckutzne at gwdg.de>> wrote:
>
> gmx mdrun -membed membed.dat
>
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-- 
Reid C. Van Lehn
Alfredo Alexander-Katz Research Group
http://soft-materials.scripts.mit.edu/www/member.shtml?member=reid
Ph.D Candidate - Materials Science