diff --git a/examples/PACKAGES/imd/deca-ala-solv_imd_v3.py b/examples/PACKAGES/imd/deca-ala-solv_imd_v3.py new file mode 100644 index 0000000000..176e15e811 --- /dev/null +++ b/examples/PACKAGES/imd/deca-ala-solv_imd_v3.py @@ -0,0 +1,13 @@ +""" +For use with 'in.deca-ala-solv_imd_v3'. + +Tested with imdclient v0.1.4 and MDAnalysis v2.8.0 +""" +from imdclient.IMD import IMDReader +import MDAnalysis as mda + +u = mda.Universe('data.deca-ala-solv', "imd://localhost:5678", topology_format='DATA') + +for ts in u.trajectory: + print(ts.time) + print(ts.velocities) \ No newline at end of file diff --git a/examples/PACKAGES/imd/in.deca-ala-solv_imd_v3 b/examples/PACKAGES/imd/in.deca-ala-solv_imd_v3 new file mode 100644 index 0000000000..a7e8244cdc --- /dev/null +++ b/examples/PACKAGES/imd/in.deca-ala-solv_imd_v3 @@ -0,0 +1,31 @@ +# +units real +neighbor 2.5 bin +neigh_modify delay 1 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 8 10 +pair_modify mix arithmetic +special_bonds charmm +read_data data.deca-ala-solv + + +group peptide id <= 103 +fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23 + +thermo 100 +thermo_style multi +timestep 2.0 +kspace_style pppm 1e-5 + +fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2 + +# IMD setup. Client code available in 'deca-ala-solv_imd_v3.py' +fix comm all imd 5678 unwrap on trate 10 version 3 time on box on coordinates on velocities on forces off + +run 5000000 \ No newline at end of file