From 8f6b8e90b78224a607187b12c933f1f71ce1f4c5 Mon Sep 17 00:00:00 2001
From: Sikorski <sikorski@zib.de>
Date: Mon, 13 May 2024 14:37:54 +0200
Subject: [PATCH] remove nacl features, default ionicstrength=0

---
 scripts/villin.jl         |  2 +-
 src/simulators/mopenmm.py | 12 ++++++------
 src/simulators/openmm.jl  |  4 ++--
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/scripts/villin.jl b/scripts/villin.jl
index 6f5bd31..62a0851 100644
--- 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
index 3172161..a30f3b0 100644
--- 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
index 6558364..c01fbde 100644
--- 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