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add examples
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‎examples/JSON/rid.json‎

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‎examples/README.md‎

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# Examples of RiD-kit
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## Ala-dipeptide
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```bash
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rid submit -i ./ala2_input -c ./rid_json_files/rid_ala2.json -m machine_bohrium_k8s.json
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```
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## Chignolin
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```bash
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rid submit -i ./chignolin_input -c ./rid_json_files/rid_chignolin.json -m machine_bohrium_k8s.json
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```
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## Hafnium Oxide reaction
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```bash
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rid submit -i ./hfo2_input -c ./rid_json_files/rid_hfo2.json -m machine_bohrium_k8s.json
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```

‎examples/ala2_input/ala2.gro‎

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‎examples/ala2_input/ala2.top‎

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;
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; File 'topol.top' was generated
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; By user: unknown (1000)
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; On host: han-x1
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; At date: Sun Dec 31 23:31:31 2017
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;
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; This is a standalone topology file
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;
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; Created by:
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; :-) GROMACS - gmx pdb2gmx, VERSION 5.1.4 (-:
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;
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; Executable: /home/wanghan/local/gromacs/5.1.4-plumed-fe/bin/gmx
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; Data prefix: /home/wanghan/local/gromacs/5.1.4-plumed-fe
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; Command line:
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; gmx pdb2gmx -f mol.pdb -ff amber99sb -water tip3p
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; Force field was read from the standard GROMACS share directory.
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;
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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 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 ; qtot 0.1123
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2 CT 1 ACE CH3 2 -0.3662 12.01 ; qtot -0.2539
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3 HC 1 ACE HH32 3 0.1123 1.008 ; qtot -0.1416
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4 HC 1 ACE HH33 4 0.1123 1.008 ; qtot -0.0293
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5 C 1 ACE C 5 0.5972 12.01 ; qtot 0.5679
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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 ; qtot -0.4157
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8 H 2 ALA H 8 0.2719 1.008 ; qtot -0.1438
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9 CT 2 ALA CA 9 0.0337 12.01 ; qtot -0.1101
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10 H1 2 ALA HA 10 0.0823 1.008 ; qtot -0.0278
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11 CT 2 ALA CB 11 -0.1825 12.01 ; qtot -0.2103
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12 HC 2 ALA HB1 12 0.0603 1.008 ; qtot -0.15
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13 HC 2 ALA HB2 13 0.0603 1.008 ; qtot -0.0897
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14 HC 2 ALA HB3 14 0.0603 1.008 ; qtot -0.0294
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15 C 2 ALA C 15 0.5973 12.01 ; qtot 0.5679
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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 ; qtot -0.4157
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18 H 3 NME H 18 0.2719 1.008 ; qtot -0.1438
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19 CT 3 NME CH3 19 -0.149 12.01 ; qtot -0.2928
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20 H1 3 NME HH31 20 0.0976 1.008 ; qtot -0.1952
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21 H1 3 NME HH32 21 0.0976 1.008 ; qtot -0.0976
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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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[ constraints ]
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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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Protein
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[ molecules ]
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; Compound #mols
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Protein 1
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SOL 383

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