remove nacl features, default ionicstrength=0

axsk · May 13, 2024 · 8f6b8e9 · 8f6b8e9
1 parent 5e865d9
commit 8f6b8e9
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/scripts/villin.jl b/scripts/villin.jl
@@ -11,7 +11,7 @@ pdb = "data/villin nowater.pdb"
 steps = 20_000
 step = 0.002
 temp = 310
-friction = 0.1
+friction = 1
 integrator = :langevinmiddle
 minimize = true
 momenta = true

diff --git a/src/simulators/mopenmm.py b/src/simulators/mopenmm.py
@@ -121,12 +121,12 @@ def get_numpy_state(context, withmomenta):
 
 def set_numpy_state(context, x, withmomenta):
     if withmomenta:
-          n = len(x) // 2
-          context.setPositions(x[:n])
-          context.setVelocities(x[n:])
-        else:
-          context.setPositions(x)
-          context.setVelocitiesToTemperature(sim.integrator.getTemperature())
+        n = len(x) // 2
+        context.setPositions(x[:n])
+        context.setVelocities(x[n:])
+    else:
+        context.setPositions(x)
+        context.setVelocitiesToTemperature(sim.integrator.getTemperature())
 
 def newcontext(context, mmthreads):
   if mmthreads == 'gpu':

diff --git a/src/simulators/openmm.jl b/src/simulators/openmm.jl
@@ -87,7 +87,7 @@ function OpenMMSimulation(;
     mmthreads=1,
     addwater=false,
     padding=3,
-    ionicstrength=0.15,
+    ionicstrength=0.0,
     forcefield_kwargs=Dict(),
     momenta=false)
 
@@ -242,7 +242,7 @@ end
 function atomfilter(atom)
     !(
         atom.element.symbol == "H" ||
-        atom.residue.name == "HOH"
+        atom.residue.name in ["HOH", "NA", "CL"]
     )
 end