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.
- The HPSTRING specifies the chemical nature of each monomer. The only supported options are Hydrophobic (H) or Polar (P).
- 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).
- 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).
- The number of replicas for replica exchange simulations. This is usually
1for enumeration simulations because those simulations do not involve random moves in conformational space.
- A list of floats that specifies the temperature (K) of each replica. The length of the REPLICATEMPS list should be equal to NREPLICAS.
- 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.
- The number of steps between replica swap attempts.
- How to swap replicas.
random pairto randomly choose two replicas to swap;
neighborsto randomly choose one replica
iand swap it with its
- Select which type of monte carlo moves will be used to sample conformational
MS1for three-bead flips and rigid rotations;
MS2for three-bead flips, crankshaft moves, and rigid rotations; and
MS3for rigid rotations only.
- 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.
- The force constant of the harmonic restraints specified in RESTRAINED_STATE.
- In a monte carlo simulation, save coordinates to trajectory after this number of steps.
- The path to the file that specifies what the native contacts are for the chain specified by HPSTRING.
- If the monte carlo simulation finds the native conformation of the chain
(as defined by the contacts in NATIVEDIR), then halt the simulation if