diff --git a/doc/fix_restrain.html b/doc/fix_restrain.html index fffc7fe3fe..8cdb789a52 100644 --- a/doc/fix_restrain.html +++ b/doc/fix_restrain.html @@ -26,15 +26,15 @@ 
  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
+    r0 = equilibrium bond distance (distance units)
+  angle args = atom1 atom2 atom3 Kstart Kstop theta0
     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
+    theta0 = equilibrium angle theta (degrees)
+  bond args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
     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) 
+    phi0 = equilibrium dihedral angle phi (degrees)
@@ -48,20 +48,22 @@ fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5

Description:

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 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 create a permanent bond or -angle or dihedral, you should modify the data file. +of a 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 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 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 -restraint coefficient. The second example applies similar restraints +

The group-ID specified by this fix is ignored. +

+

The second example above applies a restraint to hold the dihedral +angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant +restraint coefficient. The fourth example applies similar restraints to multiple dihedral angles using a restraint coefficient that increases from 0.0 to 2000.0 over the course of the run.

@@ -75,7 +77,7 @@ self-consistent minimization problem (see below).

In order for a restraint to be effective, the restraint force must typically be significantly larger than the forces associated with -conventional forcefield terms. If the restraint is applied during a +conventional forcefield terms. If the restraint is applied during a dynamics run (as opposed to during an energy minimization), a large restraint coefficient can significantly reduce the stable timestep size, especially if the atoms are initially far from the preferred @@ -85,17 +87,17 @@ works best for a given application.

For the case of finding a minimum energy structure for a single molecule with particular restratins (e.g. for fitting forcefield parameters or constructing a potential energy surface), commands such -as the following might be useful: +as the following may be useful: 

# minimize molecule energy with restraints
 velocity all create 600.0 8675309 mom yes rot yes dist gaussian
 fix NVE all nve
 fix TFIX all langevin 600.0 0.0 100 24601
-fix REST all restrain 0.0 5000.0 dihedral 2 1 3 8 $angle1 3 1 2 9 $angle2
+fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $angle1 dihedral 3 1 2 9 0.0 5000.0 $angle2
 fix_modify REST energy yes
 run 10000
 fix TFIX all langevin 0.0 0.0 100 24601
-fix REST all restrain 5000.0 5000.0 dihedral 2 1 3 8 $angle1 3 1 2 9 $angle2
+fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $angle1 dihedral 3 1 2 9 5000.0 5000.0 $angle2
 fix_modify REST energy yes
 run 10000
 # sanity check for convergence
@@ -106,19 +108,57 @@ run 0
+

The bond keyword applies a bond restraint to the specified atoms +using the same functional form used by the bond_style +harmonic command. The potential associated with +the restraint is +

+
+
+

with the following coefficients: +

+ +

K and r0 are specified with the fix. Note that the usual 1/2 factor +is included in K. +

+
+ +

The angle keyword applies an angle restraint to the specified atoms +using the same functional form used by the angle_style +harmonic command. The potential associated with +the restraint is +

+
+
+

with the following coefficients: +

+ +

K and theta0 are specified with the fix. Note that the usual 1/2 +factor is included in K. +

+
+

The dihedral keyword applies a dihedral restraint to the specified -atoms using a simplified form of the function used in dihedral_style -charmm. Specifically, the potential associated -with the restraint is +atoms using a simplified form of the function used by the +dihedral_style charmm command. The potential +associated with the restraint is

with the following coefficients:

-