[gmx-users] g_membed stops after only one iteration

maria goranovic mariagoranovic at gmail.com
Thu Aug 4 13:01:00 CEST 2011


I am trying to use g_membed to insert a protein into a bilayer. I made some
changes to the sample.mdp file downloaded from the authors' homepage. The
changes were:

- reduced time step to 0.001 ps (instead of 0.002)
- changed constraints to hbonds instead of all-bonds.

g_membed runs fine, but stops only after one iteration after which the
protein is of course shrunk. The command used is:

echo 20 16 | g_membed -f membed.tpr  -n membed.ndx -xyinit 0.1 -xyend 1.0
-nxy 1000 -maxwarn 10

I am wondering what is going on ?

Also, is there a way to parallelize g_membed?

Maria G.
Technical University of Denmark
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