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ML/MM with GROMACS and Metatomic
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‎docs/src/software/gromacs.sec‎

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@@ -15,3 +15,4 @@ comprehensive suite for MD workflows. Its open-source nature and active communit
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continuous development and support.
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- examples/water-pulsed/water-pulsed
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- examples/ml-mm/ml-mm

‎docs/src/topics/ml-models.sec‎

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- examples/flashmd/flashmd-demo
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- examples/shiftml/shiftml-example
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- examples/hamiltonian-qm7/hamiltonian-qm7
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- examples/ml-mm/ml-mm

‎docs/src/topics/universal.sec‎

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@@ -11,3 +11,4 @@ structural space.
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- examples/pet-mad-uq/pet-mad-uq
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- examples/flashmd/flashmd-demo
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- examples/eon-pet-neb/eon-pet-neb
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- examples/ml-mm/ml-mm

‎examples/ml-mm/.gitignore‎

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#*
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*.cpt
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*.edr
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*.lock
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*.log
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*.npz
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*.pt
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*.trr
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*.tpr
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confout.gro
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mdout.mdp

‎examples/ml-mm/README.rst‎

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ML-MM Simulations with GROMACS and Metatomic
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============================================
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Simulate alanine dipeptide in water using a machine learning potential for the
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solute (ML-MM simulation) with GROMACS and the Metatomic interface.

‎examples/ml-mm/data/conf.gro‎

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‎examples/ml-mm/data/topol.top‎

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; Include forcefield parameters
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#include "amber99sb.ff/forcefield.itp"
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[ moleculetype ]
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; Name nrexcl
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Protein_chain_A 3
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[ atoms ]
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; nr type resnr residue atom cgnr charge mass typeB chargeB massB
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; residue 1 ACE rtp ACE q 0.0
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1 HC 1 ACE HH31 1 0.1123 1.008
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2 CT 1 ACE CH3 2 -0.3662 12.01
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3 HC 1 ACE HH32 3 0.1123 1.008
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4 HC 1 ACE HH33 4 0.1123 1.008
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5 C 1 ACE C 5 0.5972 12.01
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6 O 1 ACE O 6 -0.5679 16 ; qtot 0
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; residue 2 ALA rtp ALA q 0.0
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7 N 2 ALA N 7 -0.4157 14.01
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8 H 2 ALA H 8 0.2719 1.008
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9 CT 2 ALA CA 9 0.0337 12.01
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10 H1 2 ALA HA 10 0.0823 1.008
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11 CT 2 ALA CB 11 -0.1825 12.01
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12 HC 2 ALA HB1 12 0.0603 1.008
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13 HC 2 ALA HB2 13 0.0603 1.008
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14 HC 2 ALA HB3 14 0.0603 1.008
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15 C 2 ALA C 15 0.5973 12.01
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16 O 2 ALA O 16 -0.5679 16 ; qtot 0
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; residue 3 NME rtp NME q 0.0
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17 N 3 NME N 17 -0.4157 14.01
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18 H 3 NME H 18 0.2719 1.008
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19 CT 3 NME CH3 19 -0.149 12.01
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20 H1 3 NME HH31 20 0.0976 1.008
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21 H1 3 NME HH32 21 0.0976 1.008
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22 H1 3 NME HH33 22 0.0976 1.008 ; qtot 0
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[ bonds ]
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; ai aj funct c0 c1 c2 c3
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1 2 1
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2 3 1
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2 4 1
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2 5 1
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5 6 1
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5 7 1
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7 8 1
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7 9 1
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9 10 1
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9 11 1
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9 15 1
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11 12 1
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11 13 1
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11 14 1
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15 16 1
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15 17 1
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17 18 1
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17 19 1
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19 20 1
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19 21 1
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19 22 1
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[ pairs ]
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; ai aj funct c0 c1 c2 c3
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1 6 1
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1 7 1
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2 8 1
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2 9 1
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3 6 1
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3 7 1
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4 6 1
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4 7 1
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5 10 1
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5 11 1
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5 15 1
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6 8 1
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6 9 1
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7 12 1
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7 13 1
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7 14 1
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7 16 1
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7 17 1
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8 10 1
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8 11 1
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8 15 1
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9 18 1
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9 19 1
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10 12 1
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10 13 1
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10 14 1
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10 16 1
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10 17 1
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11 16 1
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11 17 1
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12 15 1
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13 15 1
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14 15 1
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15 20 1
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15 21 1
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15 22 1
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16 18 1
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16 19 1
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18 20 1
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18 21 1
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18 22 1
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[ angles ]
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; ai aj ak funct c0 c1 c2 c3
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1 2 3 1
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1 2 4 1
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1 2 5 1
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3 2 4 1
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3 2 5 1
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4 2 5 1
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2 5 6 1
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2 5 7 1
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6 5 7 1
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5 7 8 1
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5 7 9 1
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8 7 9 1
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7 9 10 1
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7 9 11 1
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7 9 15 1
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10 9 11 1
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10 9 15 1
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11 9 15 1
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9 11 12 1
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9 11 13 1
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9 11 14 1
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12 11 13 1
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12 11 14 1
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13 11 14 1
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9 15 16 1
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9 15 17 1
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16 15 17 1
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15 17 18 1
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15 17 19 1
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18 17 19 1
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17 19 20 1
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17 19 21 1
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17 19 22 1
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20 19 21 1
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20 19 22 1
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21 19 22 1
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[ dihedrals ]
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; ai aj ak al funct c0 c1 c2 c3 c4 c5
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1 2 5 6 9
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1 2 5 7 9
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3 2 5 6 9
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3 2 5 7 9
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4 2 5 6 9
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4 2 5 7 9
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2 5 7 8 9
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2 5 7 9 9
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6 5 7 8 9
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6 5 7 9 9
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5 7 9 10 9
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5 7 9 11 9
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5 7 9 15 9
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8 7 9 10 9
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8 7 9 11 9
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8 7 9 15 9
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7 9 11 12 9
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7 9 11 13 9
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7 9 11 14 9
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10 9 11 12 9
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10 9 11 13 9
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10 9 11 14 9
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15 9 11 12 9
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15 9 11 13 9
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15 9 11 14 9
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7 9 15 16 9
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7 9 15 17 9
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10 9 15 16 9
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10 9 15 17 9
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11 9 15 16 9
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11 9 15 17 9
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9 15 17 18 9
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9 15 17 19 9
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16 15 17 18 9
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16 15 17 19 9
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15 17 19 20 9
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15 17 19 21 9
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15 17 19 22 9
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18 17 19 20 9
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18 17 19 21 9
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18 17 19 22 9
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[ dihedrals ]
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; ai aj ak al funct c0 c1 c2 c3
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2 7 5 6 4
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5 9 7 8 4
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9 17 15 16 4
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15 19 17 18 4
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; Include Position restraint file
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#ifdef POSRES
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#include "posre.itp"
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#endif
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; Include water topology
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#include "amber99sb.ff/tip3p.itp"
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#ifdef POSRES_WATER
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; Position restraint for each water oxygen
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[ position_restraints ]
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; i funct fcx fcy fcz
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1 1 1000 1000 1000
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#endif
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; Include topology for ions
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#include "amber99sb.ff/ions.itp"
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[ system ]
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; Name
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Alanine dipeptide in water
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[ molecules ]
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; Compound #mols
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Protein_chain_A 1
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SOL 2255

‎examples/ml-mm/environment.yml‎

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channels:
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- conda-forge
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dependencies:
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- chemiscope
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- gromacs
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- mdanalysis
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- metatrain
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- python=3.12

‎examples/ml-mm/grompp.mdp‎

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; Run control
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integrator = md
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dt = 0.0005
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nsteps = 500
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; Output control
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nstxout = 10
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nstvout = 10
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nstenergy = 10
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nstcalcenergy = 10
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nstlog = 10
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; Neighborsearching
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cutoff-scheme = Verlet
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pbc = xyz
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; Electrostatics
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coulombtype = PME
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; Temperature coupling
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tcoupl = v-rescale
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tc-grps = water protein ; two coupling groups - more accurate
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tau-t = 2.0 2.0 ; time constant, in ps
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ref-t = 300 300
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; Metatomic interface
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; metatomic-active = yes
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; metatomic-input-group = protein ; the group on which ML forces are applied
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; metatomic-modelfile = pet-mad-v1.0.2.pt ; path to the ML model file
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; metatomic-device = cpu ; device to run the ML model on (cpu or cuda)

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