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Difference between revisions of "Replica Exchange Condition File Examples"
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| − | + | __NOTOC__ | |
| − | + | Below is a list of examples for various condition files | |
| − | Below is a list of examples for various condition files | ||
==Hamiltonian Replica Exchange== | ==Hamiltonian Replica Exchange== | ||
===Dihedral Restraint=== | ===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. | ||
<pre> | <pre> | ||
bias dihe | 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=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 | ||
| + | </pre> | ||
| + | |||
| + | ===Radius of Gyration Restraint=== | ||
| + | |||
| + | A radius of gyration restraint is applied. | ||
| + | |||
| + | <pre> | ||
| + | bias rg | ||
| + | 298 force=10,target=0 | ||
| + | 298 force=10,target=10 | ||
| + | 298 force=10,target=20 | ||
| + | 298 force=10,target=30 | ||
| + | </pre> | ||
| + | |||
| + | ===RMSD Restraint=== | ||
| + | |||
| + | <pre> | ||
| + | bias rmsd | ||
| + | </pre> | ||
| + | |||
| + | ===HMCM Restraint=== | ||
| + | |||
| + | <pre> | ||
| + | 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 | ||
| + | |||
</pre> | </pre> | ||
Latest revision as of 18:11, 6 August 2009
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