Merge pull request #4431 from Becksteinlab/imd-v3-integration

Interactive Molecular Dynamics [IMD] Version 3 implementation

examples/PACKAGES/imd/deca-ala-solv_imd_v3.py

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+"""
+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)

examples/PACKAGES/imd/in.deca-ala-solv_imd_v3

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+# 
+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