# Configuration File FormatΒΆ

*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`.