Problem with energy exclusion groups using gmx mdrun -membed

GROMACS version: 2021
GROMACS modification: No

Dear all,

I have been trying to insert a protein into a preequilibrated membrane using the gmx mdrun -membed option. Most of it seems to be fine but I keep getting these two messages:

Warning 1:
The number of growth steps (-nxy + -nz) is larger than the number of steps in the tpr.
(increase maxwarn in the membed input file to override)


Program: gmx mdrun, version 2021.1
Source file: src/gromacs/mdlib/membed.cpp (line 1248)

Input error or input inconsistency:
No energy exclusion groups defined. This is necessary for energy exclusion in
the freeze group


To be honest, I am pretty new to MD, so I don’t quite understand the first one. I guess my .mdp file, as it does not contain any nsteps (as the .dat file for -membed shoudl take care of this, or so I understand) gives that error, but I think it should not be important.

The second one I cannot understand it at all. My .mdp file does contain energy exclusion groups with the same name they appear in the index.ndx file:

Here the .mdp:

integrator = md
energygrps = PROTEIN
freezegrps = PROTEIN
freezedim = Y Y Y
energygrp_excl = PROTEIN PROTEIN

Here the selection in the terminal when running -membed based on the index.ndx file:

Select a group to embed in the membrane:
Group 0 ( System) has 51585 elements
Group 1 ( PROTEIN) has 3519 elements
Group 2 ( SOLVENT) has 42050 elements
Group 3 ( MEMBRANE) has 6016 elements
Select a group: 1
Selected 1: ‘PROTEIN’

Select a group to embed PROTEIN into (e.g. the membrane):
Group 0 ( System) has 51585 elements
Group 1 ( PROTEIN) has 3519 elements
Group 2 ( SOLVENT) has 42050 elements
Group 3 ( MEMBRANE) has 6016 elements
Select a group: 3
Selected 3: ‘MEMBRANE’

Any idea why this might be happening? Any advice would me much appreciated.

Thank you!

Kind regards,

Dr Mario López

Hi

this old post may be useful

The option is not support in the current version of GROMACS.
The feature for embedding a protein in a membrane will be retained, but probably in a different form, such as gmx membed (see release note Changes anticipated to GROMACS 2021 functionality — GROMACS 2021.1 documentation)

An alternative to embed a protein in a lipid bilayer is CHARMM-GUI.

Best regards
Alessandra

Hi Alessandra,

Thanks a lot for your reply. I understand then that -embed is not functional in the 2020-2021 versions of GROMACS (as it requires defining energy groups to run)? That a let-down.

Thanks for your suggestion. I wanted to use a complex pre-equilibrated bilayer with lipids not available in CHARMM-GUI, but as I can’t manage to make -membed nor any of the popular alternatives work I would probably rethink the membrane composition and go with that.

Thanks!