Difference between revisions of "Replica Exchange Condition File Examples"

Revision as of 15:35, 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.

bias dihe
300 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

Radius of Gyration Restraint

bias rgyr

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.
 <pre>
@@ Line 14: / Line 14: @@
 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===
+<pre>
+bias rgyr
+</pre>
+===RMSD Restraint===
+<pre>
+bias rmsd
+</pre>
+===HMCM Restraint===
+<pre>
+bias hmcm
 </pre>