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ML/MM with GROMACS and Metatomic #197

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ML/MM with GROMACS and Metatomic
PicoCentauri Dec 9, 2025
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Merge branch 'main' into mts-gromacs
PicoCentauri Dec 10, 2025
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1 change: 1 addition & 0 deletions docs/src/software/gromacs.sec
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Expand Up @@ -15,3 +15,4 @@ comprehensive suite for MD workflows. Its open-source nature and active communit
continuous development and support.

- examples/water-pulsed/water-pulsed
- examples/ml-mm/ml-mm
1 change: 1 addition & 0 deletions docs/src/topics/ml-models.sec
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Expand Up @@ -18,3 +18,4 @@ data.
- examples/flashmd/flashmd-demo
- examples/shiftml/shiftml-example
- examples/hamiltonian-qm7/hamiltonian-qm7
- examples/ml-mm/ml-mm
1 change: 1 addition & 0 deletions docs/src/topics/universal.sec
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Expand Up @@ -11,3 +11,4 @@ structural space.
- examples/pet-mad-uq/pet-mad-uq
- examples/flashmd/flashmd-demo
- examples/eon-pet-neb/eon-pet-neb
- examples/ml-mm/ml-mm
11 changes: 11 additions & 0 deletions examples/ml-mm/.gitignore
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#*
*.cpt
*.edr
*.lock
*.log
*.npz
*.pt
*.trr
*.tpr
confout.gro
mdout.mdp
5 changes: 5 additions & 0 deletions examples/ml-mm/README.rst
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ML-MM Simulations with GROMACS and Metatomic
============================================

Simulate alanine dipeptide in water using a machine learning potential for the
solute (ML-MM simulation) with GROMACS and the Metatomic interface.
6,790 changes: 6,790 additions & 0 deletions examples/ml-mm/data/conf.gro
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219 changes: 219 additions & 0 deletions examples/ml-mm/data/topol.top
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; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"

[ moleculetype ]
; Name nrexcl
Protein_chain_A 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 ACE rtp ACE q 0.0
1 HC 1 ACE HH31 1 0.1123 1.008
2 CT 1 ACE CH3 2 -0.3662 12.01
3 HC 1 ACE HH32 3 0.1123 1.008
4 HC 1 ACE HH33 4 0.1123 1.008
5 C 1 ACE C 5 0.5972 12.01
6 O 1 ACE O 6 -0.5679 16 ; qtot 0
; residue 2 ALA rtp ALA q 0.0
7 N 2 ALA N 7 -0.4157 14.01
8 H 2 ALA H 8 0.2719 1.008
9 CT 2 ALA CA 9 0.0337 12.01
10 H1 2 ALA HA 10 0.0823 1.008
11 CT 2 ALA CB 11 -0.1825 12.01
12 HC 2 ALA HB1 12 0.0603 1.008
13 HC 2 ALA HB2 13 0.0603 1.008
14 HC 2 ALA HB3 14 0.0603 1.008
15 C 2 ALA C 15 0.5973 12.01
16 O 2 ALA O 16 -0.5679 16 ; qtot 0
; residue 3 NME rtp NME q 0.0
17 N 3 NME N 17 -0.4157 14.01
18 H 3 NME H 18 0.2719 1.008
19 CT 3 NME CH3 19 -0.149 12.01
20 H1 3 NME HH31 20 0.0976 1.008
21 H1 3 NME HH32 21 0.0976 1.008
22 H1 3 NME HH33 22 0.0976 1.008 ; qtot 0

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
2 3 1
2 4 1
2 5 1
5 6 1
5 7 1
7 8 1
7 9 1
9 10 1
9 11 1
9 15 1
11 12 1
11 13 1
11 14 1
15 16 1
15 17 1
17 18 1
17 19 1
19 20 1
19 21 1
19 22 1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 6 1
1 7 1
2 8 1
2 9 1
3 6 1
3 7 1
4 6 1
4 7 1
5 10 1
5 11 1
5 15 1
6 8 1
6 9 1
7 12 1
7 13 1
7 14 1
7 16 1
7 17 1
8 10 1
8 11 1
8 15 1
9 18 1
9 19 1
10 12 1
10 13 1
10 14 1
10 16 1
10 17 1
11 16 1
11 17 1
12 15 1
13 15 1
14 15 1
15 20 1
15 21 1
15 22 1
16 18 1
16 19 1
18 20 1
18 21 1
18 22 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1
1 2 4 1
1 2 5 1
3 2 4 1
3 2 5 1
4 2 5 1
2 5 6 1
2 5 7 1
6 5 7 1
5 7 8 1
5 7 9 1
8 7 9 1
7 9 10 1
7 9 11 1
7 9 15 1
10 9 11 1
10 9 15 1
11 9 15 1
9 11 12 1
9 11 13 1
9 11 14 1
12 11 13 1
12 11 14 1
13 11 14 1
9 15 16 1
9 15 17 1
16 15 17 1
15 17 18 1
15 17 19 1
18 17 19 1
17 19 20 1
17 19 21 1
17 19 22 1
20 19 21 1
20 19 22 1
21 19 22 1

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 5 6 9
1 2 5 7 9
3 2 5 6 9
3 2 5 7 9
4 2 5 6 9
4 2 5 7 9
2 5 7 8 9
2 5 7 9 9
6 5 7 8 9
6 5 7 9 9
5 7 9 10 9
5 7 9 11 9
5 7 9 15 9
8 7 9 10 9
8 7 9 11 9
8 7 9 15 9
7 9 11 12 9
7 9 11 13 9
7 9 11 14 9
10 9 11 12 9
10 9 11 13 9
10 9 11 14 9
15 9 11 12 9
15 9 11 13 9
15 9 11 14 9
7 9 15 16 9
7 9 15 17 9
10 9 15 16 9
10 9 15 17 9
11 9 15 16 9
11 9 15 17 9
9 15 17 18 9
9 15 17 19 9
16 15 17 18 9
16 15 17 19 9
15 17 19 20 9
15 17 19 21 9
15 17 19 22 9
18 17 19 20 9
18 17 19 21 9
18 17 19 22 9

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
2 7 5 6 4
5 9 7 8 4
9 17 15 16 4
15 19 17 18 4

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "amber99sb.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include "amber99sb.ff/ions.itp"

[ system ]
; Name
Alanine dipeptide in water

[ molecules ]
; Compound #mols
Protein_chain_A 1
SOL 2255
8 changes: 8 additions & 0 deletions examples/ml-mm/environment.yml
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channels:
- conda-forge
dependencies:
- chemiscope
- gromacs
- mdanalysis
- metatrain
- python=3.12
30 changes: 30 additions & 0 deletions examples/ml-mm/grompp.mdp
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; Run control
integrator = md
dt = 0.0005
nsteps = 500

; Output control
nstxout = 10
nstvout = 10
nstenergy = 10
nstcalcenergy = 10
nstlog = 10

; Neighborsearching
cutoff-scheme = Verlet
pbc = xyz

; Electrostatics
coulombtype = PME

; Temperature coupling
tcoupl = v-rescale
tc-grps = water protein ; two coupling groups - more accurate
tau-t = 2.0 2.0 ; time constant, in ps
ref-t = 300 300

; Metatomic interface
; metatomic-active = yes
; metatomic-input-group = protein ; the group on which ML forces are applied
; metatomic-modelfile = pet-mad-v1.0.2.pt ; path to the ML model file
; metatomic-device = cpu ; device to run the ML model on (cpu or cuda)
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