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Difference between revisions of "Replica Exchange Condition File Examples"
From MMTSB
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===Radius of Gyration Restraint=== | ===Radius of Gyration Restraint=== | ||
| + | |||
| + | A radius of gyration restraint is applied. | ||
<pre> | <pre> | ||
| − | bias | + | bias rg |
| + | 298 force=10,target=0 | ||
| + | 298 force=10,target=10 | ||
| + | 298 force=10,target=20 | ||
| + | 298 force=10,target=30 | ||
</pre> | </pre> | ||
Revision as of 15:37, 29 July 2009
Contents
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
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