Replica Exchange Condition File Examples

Below is a list of examples for various condition files

Hamiltonian Replica Exchange

Dihedral Restraint

A center-of-mass dihedral restraint is applied to each replica with a force 100kcal/mol/rad/rad and different target dihedral angle values. Four selections are required to define a dihedral angle. This uses an MMFP GEO potential. All replicas are simulated at a temperature of 300K.

bias dihe
300 force=100,target=0,sel1=N01E:11.base,sel2=N01F:20.sugar,sel3=N01F:21.sugar,sel4=N01F:21.base
300 force=100,target=10,sel1=N01E:11.base,sel2=N01F:20.sugar,sel3=N01F:21.sugar,sel4=N01F:21.base
300 force=100,target=20,sel1=N01E:11.base,sel2=N01F:20.sugar,sel3=N01F:21.sugar,sel4=N01F:21.base

Radius of Gyration Restraint

A radius of gyration restraint is applied.

bias rg
298 force=10,target=0
298 force=10,target=10
298 force=10,target=20
298 force=10,target=30

RMSD Restraint

bias rmsd

HMCM Restraint

bias hmcm
300 force=200,target=0.0,refx=31.27276,refy=7.82891,refz=-18.54366,selection=N01F:21
300 force=200,target=0.0,refx=31.53459,refy=8.41458,refz=-16.64812,selection=N01F:21
300 force=200,target=0.0,refx=29.63026,refy=6.53479,refz=-18.01094,selection=N01F:21