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Replica Exchange Condition File Examples
From MMTSB
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