temoa-g1-g4_asyncre.cntl

#The job transport is the mean in which replicas are executed on GPU devices
#LOCAL_OPENMM is the only job transport system currently supported. Each local GPU is
#managed by a different process using the python multiprocessing module 
JOB_TRANSPORT = 'LOCAL_OPENMM'

#The basename of the job. Input amber files are expected to be called <jobname>.prmtop and <jobname>.inpcrd
#The checkpoint file is expected to be called <jobname>_0.xml
BASENAME = 'temoa-g1-g4'

#Arrays of thermodynamic states in temperature and alchemical space.
TEMPERATURES = '300'
LAMBDAS =    '0.00, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50, 0.50, 0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 1.00'
DIRECTION=   '   1,    1,    1,    1,    1,    1,    1,    1,    1,    1,    1,   -1,   -1,   -1,   -1,   -1,   -1,   -1,   -1,   -1,   -1,   -1'
INTERMEDIATE='   0,    0,    0,    0,    0,    0,    0,    0,    0,    0,    1,    1,    0,    0,    0,    0,    0,    0,    0,    0,    0,    0'
LAMBDA1 =    '0.00, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00'
LAMBDA2 =    '0.00, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00'
ALPHA =      '0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00'
U0 =         '0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00'
W0COEFF =    '0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00'

#The displacement vector that brings the ligand from the binding site to a position in the bulk
DISPLACEMENT = '22.00, 22.00, 22.00'

#Execution time in minutes
WALL_TIME = 240

#Frequency of replica exchange attempts in seconds
CYCLE_TIME = 10

#Frequency of saving checkpoint files in seconds
CHECKPOINT_TIME = 600

#The nodefile. Each line corresponds to a GPU device.
NODEFILE = 'nodefile'

#Number of replicas to keep in a fast execution queue. It is expressed as a fraction of the number of compute devices.
#With one device a value of 1 here keeps one replica in the queue. 
SUBJOBS_BUFFER_SIZE = '1.0'

#MD steps per replica
PRODUCTION_STEPS = '20000'

#frequency of printing information after a replica run. Must be a multiple of PRODUCTION_STEPS
PRNT_FREQUENCY = '20000'

#frequency of saving trajectory frames. Must be a multiple of PRODUCTION_STEPS
TRJ_FREQUENCY = '20000'

#list of ligand atoms. The equil.py script prints these out.
LIGAND1_ATOMS = 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216
LIGAND2_ATOMS = 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233

#list of atoms of the ligand that define the centroid of the ligand. The equil.py script prints these out.
LIGAND1_CM_ATOMS = 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216
LIGAND2_CM_ATOMS = 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233

#list of atoms of the ligand that define the centroid of the ligand. The mdlambda.py script prints these out.
RCPT_CM_ATOMS = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195

#force constant (in kcal/(mol A^2)) and tolerance (in A) of the binding site restraint potential
CM_KF = 25.00
CM_TOL = 5.00

#alignment restraint settings, reference atoms are give in molecular indexes. Force constants
#in kcal/(mol A^2) or kcal/(mol deg^2) or 
ALIGN_LIGAND1_REF_ATOMS = 8, 6, 4 
ALIGN_LIGAND2_REF_ATOMS = 3, 5, 1
ALIGN_KF_SEP = 2.5
ALIGN_K_THETA = 10.0
ALIGN_K_PSI = 10.0


#list of atoms that are restrained followed by the corresponding force constant and tolerance,
#in kcal/(mol A^2) and angstroms, respectively
POS_RESTRAINED_ATOMS = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39
POSRE_FORCE_CONSTANT = 25.0
POSRE_TOLERANCE = 0.5

#softcore parameters in kcal/mol, acore is dimensionless
UMAX = 100.00
ACORE = 0.062500
UBCORE = 50.0

#thermostat friction coefficient in 1/ps
FRICTION_COEFF = 0.500000

#MD time step in ps
TIME_STEP = 0.002

#OpenMM platform 
OPENMM_PLATFORM = CPU

#set to 'yes' to turn on verbose logging
VERBOSE = 'no'