Merge pull request #273 from jchodera/mhc-optimize

Updates to number of alchemical states for MHC example
choderalab · Jul 4, 2015 · cb8ec4e · cb8ec4e
2 parents 839e7fc + 74a31e0
commit cb8ec4e
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Showing 2 changed files with 12 additions and 4 deletions.
diff --git a/Yank/alchemy.py b/Yank/alchemy.py
@@ -353,13 +353,21 @@ def defaultComplexProtocolImplicit(cls):
         alchemical_states = list()
 
         alchemical_states.append(AlchemicalState(1.00, 1.00, 1.00, 1.)) # fully interacting
+        alchemical_states.append(AlchemicalState(1.00, 0.99, 0.99, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.98, 0.98, 1.))
         alchemical_states.append(AlchemicalState(1.00, 0.97, 0.97, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.96, 0.96, 1.))
         alchemical_states.append(AlchemicalState(1.00, 0.95, 0.95, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.94, 0.94, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.93, 0.93, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.92, 0.92, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.91, 0.91, 1.))
         alchemical_states.append(AlchemicalState(1.00, 0.90, 0.90, 1.))
-        alchemical_states.append(AlchemicalState(1.00, 0.87, 0.87, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.88, 0.88, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.86, 0.86, 1.))
         alchemical_states.append(AlchemicalState(1.00, 0.84, 0.84, 1.))
-        alchemical_states.append(AlchemicalState(1.00, 0.80, 0.80, 1.))
-        alchemical_states.append(AlchemicalState(1.00, 0.77, 0.77, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.81, 0.81, 1.))
+        alchemical_states.append(AlchemicalState(1.00, 0.78, 0.78, 1.))
         alchemical_states.append(AlchemicalState(1.00, 0.74, 0.74, 1.))
         alchemical_states.append(AlchemicalState(1.00, 0.70, 0.70, 1.))
         alchemical_states.append(AlchemicalState(1.00, 0.60, 0.60, 1.))

diff --git a/examples/mhc-peptide-tcr/run-torque.sh b/examples/mhc-peptide-tcr/run-torque.sh
@@ -16,7 +16,7 @@
 #
 # nodes: number of nodes
 #   ppn: how many cores per node to use
-#PBS -l nodes=5:ppn=4:gpus=4:shared
+#PBS -l nodes=7:ppn=4:gpus=4:shared
 ##PBS -l procs=16,gpus=1:shared
 ##PBS -l procs=8,gpus=1:shared
 #