Syntax:
-fix ID group-ID restrain Kstart Kstop keyword value(s) +fix ID group-ID restrain keyword args ...
dihedral value = atom1 atom2 atom3 atom4 target - atom1,atom2,atom3,atom4 = IDs of 4 atoms in restrained dihedral - target = target value for specified dihedral angle (degrees) +bond args = atom1 atom2 Kstart Kstop r0 + atom1,atom2 = IDs of 2 atoms in bond + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + r0 = target value for bond distance (distance units) + angle args = atom1 atom2 atom3 Kstart Kstop theta + atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + theta = target value for angle theta (degrees) + bond args = atom1 atom2 atom3 atom4 Kstart Kstop phi + atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + phi = target value for dihedral angle phi (degrees)
Examples:
-fix holdem all restrain 2000.0 2000.0 dihedral 1 2 3 4 120.0 -fix texas_holdem all restrain 0.0 2000.0 dihedral 1 2 3 4 120.0 1 2 3 5 -120.0 1 2 3 6 0.0 +fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 +fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0 +fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0 +fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0Description:
-Restrain the motion of the specified atoms by making them part of a -bond or angle or dihedral interaction whose strength can vary over +
Restrain the motion of the specified sets of atoms by making them part +of bond or angle or dihedral interaction whose strength can vary over time during a simulation. This is functionally equivalent to creating -a bond or angle or dihedral for the atoms in a data file, as specified -by the read_data command, albeit with a time-varying -pre-factor coefficient. For the purpose of forcefield +a bond or angle or dihedral for the same atoms in a data file, as +specified by the read_data command, albeit with a +time-varying pre-factor coefficient. For the purpose of forcefield parameter-fitting or mapping a molecular potential energy surface, this fix reduces the hassle and risk associated with modifying data files. In other words, use this fix to temporarily force a molecule -to adopt a particular conformation. To form a permanent bond or angle -or dihedral, modify the data file. +to adopt a particular conformation. To create a permanent bond or +angle or dihedral, you should modify the data file.
The first example above applies a restraint to hold the dihedral angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant diff --git a/doc/fix_restrain.txt b/doc/fix_restrain.txt index f70eded736..a34b5a7a77 100644 --- a/doc/fix_restrain.txt +++ b/doc/fix_restrain.txt @@ -10,37 +10,46 @@ fix restrain command :h3 [Syntax:] -fix ID group-ID restrain Kstart Kstop keyword value(s) :pre +fix ID group-ID restrain keyword args ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l restrain = style name of this fix command :l -Kstart, Kstop = restraint coefficient at start/end of run (energy -units) :l -one keyword with one or more sets of parameter values may be appended to args :l -keyword = {dihedral} :l - {dihedral} value = atom1 atom2 atom3 atom4 target - atom1,atom2,atom3,atom4 = IDs of 4 atoms in restrained dihedral - target = target value for specified dihedral angle (degrees) :pre +one or more keyword/arg pairs may be appended :l +keyword = {bond} or {angle} or {dihedral} :l + {bond} args = atom1 atom2 Kstart Kstop r0 + atom1,atom2 = IDs of 2 atoms in bond + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + r0 = target value for bond distance (distance units) + {angle} args = atom1 atom2 atom3 Kstart Kstop theta + atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + theta = target value for angle theta (degrees) + {bond} args = atom1 atom2 atom3 atom4 Kstart Kstop phi + atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + phi = target value for dihedral angle phi (degrees) :pre :ule [Examples:] -fix holdem all restrain 2000.0 2000.0 dihedral 1 2 3 4 120.0 -fix texas_holdem all restrain 0.0 2000.0 dihedral 1 2 3 4 120.0 1 2 3 5 -120.0 1 2 3 6 0.0 :pre +fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 +fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0 +fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0 +fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 :pre [Description:] -Restrain the motion of the specified atoms by making them part of a -bond or angle or dihedral interaction whose strength can vary over +Restrain the motion of the specified sets of atoms by making them part +of bond or angle or dihedral interaction whose strength can vary over time during a simulation. This is functionally equivalent to creating -a bond or angle or dihedral for the atoms in a data file, as specified -by the "read_data"_read_data.html command, albeit with a time-varying -pre-factor coefficient. For the purpose of forcefield +a bond or angle or dihedral for the same atoms in a data file, as +specified by the "read_data"_read_data.html command, albeit with a +time-varying pre-factor coefficient. For the purpose of forcefield parameter-fitting or mapping a molecular potential energy surface, this fix reduces the hassle and risk associated with modifying data files. In other words, use this fix to temporarily force a molecule -to adopt a particular conformation. To form a permanent bond or angle -or dihedral, modify the data file. +to adopt a particular conformation. To create a permanent bond or +angle or dihedral, you should modify the data file. The first example above applies a restraint to hold the dihedral angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant