From 74a31e019075143ba9bb875bffe58f5476bbc0a8 Mon Sep 17 00:00:00 2001 From: John Chodera Date: Thu, 25 Jun 2015 22:31:14 -0400 Subject: [PATCH] Updates to number of alchemical states for MHC example. --- Yank/alchemy.py | 14 +++++++++++--- examples/mhc-peptide-tcr/run-torque.sh | 2 +- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/Yank/alchemy.py b/Yank/alchemy.py index ddbd49cb..262862d0 100644 --- 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 index 6a19f6d3..f76cf8f4 100755 --- 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 #