Difference between revisions of "Replica Exchange Condition File Examples"

Revision as of 15:38, 29 July 2009

Description

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

@@ Line 7: / Line 7: @@
 ===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.
+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.
 <pre>
 bias dihe
 force=100,target=0,sel1=N01E:11.base,sel2=N01F:20.sugar,sel3=N01F:21.sugar,sel4=N01F:21.base
 force=100,target=10,sel1=N01E:11.base,sel2=N01F:20.sugar,sel3=N01F:21.sugar,sel4=N01F:21.base
 force=100,target=20,sel1=N01E:11.base,sel2=N01F:20.sugar,sel3=N01F:21.sugar,sel4=N01F:21.base
 </pre>
 ===Radius of Gyration Restraint===