diff --git a/vcell-client/src/main/java/cbit/vcell/client/ClientRequestManager.java b/vcell-client/src/main/java/cbit/vcell/client/ClientRequestManager.java
index dcd6f56719..14c8d7ff86 100644
--- a/vcell-client/src/main/java/cbit/vcell/client/ClientRequestManager.java
+++ b/vcell-client/src/main/java/cbit/vcell/client/ClientRequestManager.java
@@ -3196,6 +3196,7 @@ private void openAfterChecking(VCDocumentInfo documentInfo, final TopLevelWindow
 						boolean bRuleBased = true;
 						SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("temp NFSim app",
 								SimulationContext.Application.RULE_BASED_STOCHASTIC);
+						ruleBasedSimContext.setUsingConcentration(bngUnitSystem.isConcentration(), false);
 						List<SimulationContext> appList = new ArrayList<SimulationContext>();
 						appList.add(ruleBasedSimContext);
 
diff --git a/vcell-core/src/main/java/cbit/vcell/mapping/SimulationContext.java b/vcell-core/src/main/java/cbit/vcell/mapping/SimulationContext.java
index 9ffe3c172e..2da98d91fd 100644
--- a/vcell-core/src/main/java/cbit/vcell/mapping/SimulationContext.java
+++ b/vcell-core/src/main/java/cbit/vcell/mapping/SimulationContext.java
@@ -2984,8 +2984,11 @@ public void setUsingMassConservationModelReduction(boolean bMassConservationMode
     }
 
     public void setUsingConcentration(boolean bUseConcentration, boolean bTransformIfNeeded) throws PropertyVetoException, MappingException, MatrixException, ModelException, MathException, ExpressionException /*throws MappingException, PropertyVetoException*/{
-        if(applicationType == Application.NETWORK_STOCHASTIC || applicationType == Application.RULE_BASED_STOCHASTIC ||
-            applicationType == Application.SPRINGSALAD) {
+        if (applicationType == Application.NETWORK_STOCHASTIC ||
+                applicationType == Application.RULE_BASED_STOCHASTIC ||
+                applicationType == Application.SPRINGSALAD ||
+                (applicationType == Application.NETWORK_DETERMINISTIC && getGeometry().getDimension() == 0)
+        ) {
             boolean oldValue = bConcentration;
             if(bUseConcentration != oldValue && bTransformIfNeeded){
                 MathMapping mathMapping = createNewMathMapping();
diff --git a/vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java b/vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java
index 4585987aa5..1faed3eed4 100644
--- a/vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java
+++ b/vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java
@@ -199,18 +199,17 @@ public Object visit(ASTSeedSpecies node, Object data) {
 					SpeciesContext speciesContext = model.createSpeciesContext(structure, seedSpecies.getSpeciesPattern());
 					for(SimulationContext application : appList) {
 						SpeciesContextSpec scs = application.getReactionContext().getSpeciesContextSpec(speciesContext);
-						if (bngUnitSystem.isConcentration() && application.isUsingConcentration()){
+						if (bngUnitSystem.isConcentration() != application.isUsingConcentration()) {
+							throw new RuntimeException("BNGL model unit system is " + (bngUnitSystem.isConcentration() ? "concentration" : "count") +
+									" but application is using " + (application.isUsingConcentration() ? "concentration" : "count") +
+									". Please change the application unit system to match the model unit system.");
+						}
+						if (application.isUsingConcentration()){
 							scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).setExpression(exp);
-						}else if (!bngUnitSystem.isConcentration() && !application.isUsingConcentration()){
+						}else{
 							scs.getParameter(SpeciesContextSpec.ROLE_InitialCount).setExpression(exp);
-						}else if (!bngUnitSystem.isConcentration() && application.isUsingConcentration()){
-							Expression covertedConcentration = scs.convertParticlesToConcentration(exp);
-							scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).setExpression(covertedConcentration);
-						}else if (bngUnitSystem.isConcentration() && !application.isUsingConcentration()){
-							Expression covertedAmount = scs.convertConcentrationToParticles(exp);
-							scs.getParameter(SpeciesContextSpec.ROLE_InitialCount).setExpression(covertedAmount);
 						}
-						scs.setConstant(node.isClamped());
+						scs.setClamped(node.isClamped());
 					}
 				} catch (Exception ex) {
 					throw new RuntimeException(ex.getMessage(), ex);