Freeze group issue

GROMACS version: 2021.2
GROMACS modification: No
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Hi @jalemkul,
This is the continuation of my previous post on Freeze group: potential energy increasing.
As you suggested (and you are completely right) the issue I have with increasing the potential energy during the simulation is related to not excluding the interaction of the frozen group.
But, the main reason for not excluding the energy groups is that when I do it as:

freezegrps               = IAUM
freezedim                = Y Y Y
energygrps               =W IAUM
energygrp-excl           = IAUM IAUM

which I guess is the correct way of doing it, I get an interesting error:

ERROR 1 [file martini_md.mdp]:
  Energy group exclusions are currently not supported

This is why I had not put the Energy group exclusions in my map file as apparently they are not supported despite being mentioned in the mdp options.

I have also put the whole output of grompp here:

gmx grompp -f martini_md.mdp   -c run-short.gro   -p -o run.tpr -r run-short.gro  -maxwarn 1
                      :-) GROMACS - gmx grompp, 2021.2 (-:

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GROMACS:      gmx grompp, version 2021.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/mkhatami/uoft/gromacs/Au-C6-1ao6-1hzh-1d3k/all-elastic/full-structures/80nmbox/006-run-water-freeze
Command line:
  gmx grompp -f martini_md.mdp -c run-short.gro -p -o run.tpr -r run-short.gro -maxwarn 1

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'ns_type'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc_precision' by 'compressed-x-precision'

WARNING 1 [file martini_md.mdp]:
  You are generating velocities so I am assuming you are equilibrating a
  system. You are using Parrinello-Rahman pressure coupling, but this can
  be unstable for equilibration. If your system crashes, try equilibrating
  first with Berendsen pressure coupling. If you are not equilibrating the
  system, you can probably ignore this warning.

Setting the LD random seed to -184715285

Generated 844 of the 356590 non-bonded parameter combinations

Excluding 1 bonded neighbours molecule type 'IAUM'

Excluding 1 bonded neighbours molecule type 'W'

Velocities were taken from a Maxwell distribution at 310 K
Analysing residue names:
There are: 88663      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

NOTE 1 [file martini_md.mdp]:
  There are 18642 atoms that are fully frozen and part of COMM removal
  group(s), removing these atoms from the COMM removal group(s)

Number of degrees of freedom in T-Coupling group IAUM is 0.00
Number of degrees of freedom in T-Coupling group W is 210060.00

ERROR 1 [file martini_md.mdp]:
  Energy group exclusions are currently not supported

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K

Calculated rlist for 1x1 atom pair-list as 1.286 nm, buffer size 0.186 nm

Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.100 nm

Note that mdrun will redetermine rlist based on the actual pair-list setup

NOTE 2 [file martini_md.mdp]:
  This run will generate roughly 4275 Mb of data

There were 2 notes

There was 1 warning

Program:     gmx grompp, version 2021.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2389)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at

Just in case, here is my full mdp file:

integrator = md
dt = 0.02
nsteps = 10000000
nstcomm = 100
comm-grps =
nstlog = 1000 ; Output frequency for energies to log file
nstenergy = 1000 ; Output frequency for energies to energy file
nstxtcout = 1000 ; Output frequency for .xtc file
xtc_precision = 100
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff ;(for use with Verlet-pairlist)
rvdw = 1.1 ;(for use with Verlet-pairlist)
tcoupl = v-rescale
tc-grps = IAUM W
tau_t = 1.0 1.0
ref_t = 0 310
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p = 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4
ref_p = 1.0
gen_vel = yes
gen_temp = 310
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 6
lincs_warnangle = 30
freezegrps               = IAUM
freezedim                = Y Y Y
energygrps               =W IAUM
energygrp-excl         = IAUM IAUM
comm_mode = linear
refcoord_scaling = com

Indeed, energy group exclusions aren’t compatible with Verlet. I guess grompp should really issue a warning about this, because there is no physically sensible way to run a simulation with anything frozen. Then too, freezing is completely unphysical as it leads to inelastic collisions.