MMTSB
Tool Set Documentation

Difference between revisions of "Replica Exchange Condition File Examples"

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==Description==
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__NOTOC__
 
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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==
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===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.
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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=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
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300 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
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300 force=100,target=20,sel1=N01E:11.base,sel2=N01F:20.sugar,sel3=N01F:21.sugar,sel4=N01F:21.base
 
</pre>
 
</pre>
  
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===Radius of Gyration Restraint===
  
===Radius of Gyration Restraint===
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A radius of gyration restraint is applied.
  
 
<pre>
 
<pre>
bias rgyr
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bias rg
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298 force=10,target=0
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298 force=10,target=10
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298 force=10,target=20
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298 force=10,target=30
 
</pre>
 
</pre>
  
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<pre>
 
<pre>
 
bias hmcm
 
bias hmcm
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300 force=200,target=0.0,refx=31.27276,refy=7.82891,refz=-18.54366,selection=N01F:21
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300 force=200,target=0.0,refx=31.53459,refy=8.41458,refz=-16.64812,selection=N01F:21
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300 force=200,target=0.0,refx=29.63026,refy=6.53479,refz=-18.01094,selection=N01F:21
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</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