[gmx-users] Insertion of the protein into membrane with Gmembed

[James Starlight]

Dear Gromacs Users!



I have some questions about insertion protein into membrane with Gmembed

1) I've used default parameters from gmembed manual for preparing input for
insertion

integrator     = md
energygrp      = Protein
freezegrps     = Protein
freezedim      = Y Y Y
energygrp_table
energygrp excl = Protein Protein

Here Protein is my protein group in topology.top


I've obtained 2 warning from gropp

WARNING 1 [file gmembed.mdp, line 27]:
  Unknown left-hand 'energygrp' in parameter file



WARNING 2 [file gmembed.mdp, line 27]:
  Unknown left-hand 'energygrp excl' in parameter file

What does it means ? If I ignore those warnings I've obtain

No energy groups defined. This is necessary for energy exclusion in the
freeze group

May be I should define freezegrps as my lipid group not a protein or use
ndx file as an alternative ?

Thanks,

James
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