Problem with energy exclusion groups using gmx mdrun -membed

User discussions
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1

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

2

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 https://manual.gromacs.org/current/release-notes/2021/major/deprecated-functionality.html#gmx-mdrun-membed)

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

Best regards
Alessandra

3

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!

4

Hi Alessandra,

Is there a timeline for bringing membed functionality back? Right now I’m planning to use version 2019 to insert my protein into the membrane, then using 2023 to run my production simulations. I know there are other membrane insertion options out there, such as CHARMM-GUI, but I am hoping to do everything in GROMACS. Will this be possible any time soon?

Thank you!
Roman

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The option is not support in the current version of GROMACS.

Why do you think that Alessandra? The link you shared warns of possible changes, but does not say it’s removed, unsupported, deprecated or anything similar :-)

6

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.

It’s present and working as far as we know. Edit: I was wrong, it depends on energy-group exclusions, which was only implemented by the group scheme, which has been removed. It’s never had a test case, however, and the core developers prefer to use alternatives. I think the issue may be on your end. Are you sure you used the .mdp file that you thought you did?

Right now I’m planning to use version 2019 to insert my protein into the membrane, then using 2023 to run my production simulations

That’s a good option if there’s indeed a problem in recent versions of GROMACS. But the error you see will probably be given by GROMACS 2019 also. Do try it and see!

7

Support for energy-group exclusions has been removed because only the former group scheme supported it. However modern grompp should have rejected your attempt to do the above. How did you make your tpr file?

In any case, your plan of embedding with an older version of GROMACS and then switching to a newer version is a good one.