update atefe script

data/atefe/mor.py

@@ -0,0 +1,21 @@
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+from sys import stdout
+psf = CharmmPsfFile('/data/numerik/ag_cmd/arostami/charmm/charmm-gui(6)/charmm-gui-2501706787/openmm/step5_input.psf')
+pdb = PDBFile('/data/numerik/ag_cmd/arostami/charmm/charmm-gui(6)/charmm-gui-2501706787/openmm/step5_input.pdb')
+
+params = CharmmParameterSet('/data/numerik/ag_cmd/arostami/charmm/charmm-gui(6)/charmm-gui-2501706787/toppar/par_all36m_prot.prm', '/data/numerik/ag_cmd/arostami/charmm/charmm-gui(6)/charmm-gui-2501706787/toppar/top_all36_prot.rtf',
+                       '/data/numerik/ag_cmd/arostami/charmm/charmm-gui(6)/charmm-gui-2501706787/toppar/par_all36_lipid.prm', '/data/numerik/ag_cmd/arostami/charmm/charmm-gui(6)/charmm-gui-2501706787/toppar/top_all36_lipid.rtf',
+                       '/data/numerik/ag_cmd/arostami/charmm/charmm-gui(6)/charmm-gui-2501706787/toppar/toppar_water_ions.str', '/data/numerik/ag_cmd/arostami/charmm/charmm-gui(6)/charmm-gui-2501706787/7v7/7v7.prm', '/data/numerik/ag_cmd/arostami/charmm/charmm-gui(6)/charmm-gui-2501706787/7v7/7v7.rtf')
+
+system = psf.createSystem(params, nonbondedMethod=CutoffNonPeriodic,
+         nonbondedCutoff=1*nanometer, constraints=HBonds)
+
+integrator = LangevinIntegrator(310*kelvin,   
+                                1/picosecond, 
+                                0.002*picoseconds)
+
+simulation = Simulation(psf.topology, system, integrator)
+simulation.context.setPositions(pdb.positions)
+simulation

scripts/atefe.jl

@@ -4,7 +4,7 @@
     using CUDA
 end
 
-@time "loading" sim = OpenMMScript("data/atafe/fe/script.py", steps=10_000)
+@time "loading" sim = OpenMMScript("data/atefe/mor.py", steps=10_000)
 
 NFEATURES = 3000
 NX = 1_000