Configuration File Format

hplattice simulations require a configuration file. The file should have formatted rows consisting of two fields, separated by white-space (or any non-printing characters, like tabs):

HPSTRING                PHPPHPHPPHH
INITIALVEC              [1, 0, 1, 2, 1, 2, 1, 2, 3, 3]
EPS                     -5.0
RESTRAINED_STATE        [(1, 4), (6, 9)]
KSPRING                 0.0
NREPLICAS               9
REPLICATEMPS            [275.0, 300.0, 325.0, 350.0, 400.0, 450.0, 500.0, 600.0,    1000.0]
MCSTEPS                 1000
SWAPEVERY               50
SWAPMETHOD              random pair
MOVESET                 MS2
PRINTEVERY              1
NATIVEDIR               ../../HP-sequences/sequences/clist/hp11
STOPATNATIVE            False

Here is the full list of the parameters and what each one represents. If a parameter is not specified in the file, it will be set to a default value.

HPSTRING

The HPSTRING specifies the chemical nature of each monomer. The only supported options are Hydrophobic (H) or Polar (P).

INITIALVEC

The INITIALVEC is a list of integers that specifies the direction of the chain between two neighboring monomers: 0 (up), 1 (left), 2 (down) or 3 (right). For example, [0,0,0,0] would correspond to a 5-mer that points straight up from the origin (in the positive-y direction).

EPS

The energy of a hydrophobic contact (two H’s in adjacent lattice spaces that are not \(i+1\) or \(i+2\) neighbors along the chain).

NREPLICAS

The number of replicas for replica exchange simulations. This is usually set to 1 for enumeration simulations because those simulations do not involve random moves in conformational space.

REPLICATEMPS

A list of floats that specifies the temperature (K) of each replica. The length of the REPLICATEMPS list should be equal to NREPLICAS.

MCSTEPS

The number of monte carlo steps to run. Each replica will run for this number of steps, and they will periodically attempt to swap temperatures.

SWAPEVERY

The number of steps between replica swap attempts.

SWAPMETHOD

How to swap replicas. random pair to randomly choose two replicas to swap; neighbors to randomly choose one replica i and swap it with its i+1 neighbor.

MOVESET

Select which type of monte carlo moves will be used to sample conformational space: MS1 for three-bead flips and rigid rotations; MS2 for three-bead flips, crankshaft moves, and rigid rotations; and MS3 for rigid rotations only.

RESTRAINED_STATE

A list of tuples that specifies contacts that should be harmonically restrained. Each tuple in the list should contain a pair of integers that correspond to the indices of the monomers that should be restrained. An example would be [(1, 4), (6, 9)] which would add restraints to the monomer1-monomer4 contact and the monomer6-monomer9 contact. Note that the indices are 0-indexed, so monomer0 is the first monomer in the chain.

KSPRING

The force constant of the harmonic restraints specified in RESTRAINED_STATE.

PRINTEVERY

In a monte carlo simulation, save coordinates to trajectory after this number of steps.

NATIVEDIR

The path to the file that specifies what the native contacts are for the chain specified by HPSTRING.

STOPATNATIVE

If the monte carlo simulation finds the native conformation of the chain (as defined by the contacts in NATIVEDIR), then halt the simulation if STOPATNATIVE is True.