git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8120 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -26,15 +26,15 @@
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<PRE> <I>bond</I> args = atom1 atom2 Kstart Kstop r0
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atom1,atom2 = IDs of 2 atoms in bond
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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r0 = target value for bond distance (distance units)
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<I>angle</I> args = atom1 atom2 atom3 Kstart Kstop theta
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r0 = equilibrium bond distance (distance units)
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<I>angle</I> args = atom1 atom2 atom3 Kstart Kstop theta0
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atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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theta = target value for angle theta (degrees)
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<I>bond</I> args = atom1 atom2 atom3 atom4 Kstart Kstop phi
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theta0 = equilibrium angle theta (degrees)
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<I>bond</I> args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
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atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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phi = target value for dihedral angle phi (degrees)
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phi0 = equilibrium dihedral angle phi (degrees)
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</PRE>
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</UL>
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@ -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
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<P><B>Description:</B>
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</P>
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<P>Restrain the motion of the specified sets of atoms by making them part
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of bond or angle or dihedral interaction whose strength can vary over
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time during a simulation. This is functionally equivalent to creating
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a bond or angle or dihedral for the same atoms in a data file, as
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specified by the <A HREF = "read_data.html">read_data</A> command, albeit with a
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time-varying pre-factor coefficient. For the purpose of forcefield
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parameter-fitting or mapping a molecular potential energy surface,
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this fix reduces the hassle and risk associated with modifying data
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files. In other words, use this fix to temporarily force a molecule
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to adopt a particular conformation. To create a permanent bond or
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angle or dihedral, you should modify the data file.
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of a bond or angle or dihedral interaction whose strength can vary
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over time during a simulation. This is functionally equivalent to
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creating a bond or angle or dihedral for the same atoms in a data
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file, as specified by the <A HREF = "read_data.html">read_data</A> command, albeit
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with a time-varying pre-factor coefficient. For the purpose of
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forcefield parameter-fitting or mapping a molecular potential energy
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surface, this fix reduces the hassle and risk associated with
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modifying data files. In other words, use this fix to temporarily
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force a molecule to adopt a particular conformation. To create a
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permanent bond or angle or dihedral, you should modify the data file.
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</P>
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<P>The first example above applies a restraint to hold the dihedral angle
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formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
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restraint coefficient. The second example applies similar restraints
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<P>The group-ID specified by this fix is ignored.
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</P>
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<P>The second example above applies a restraint to hold the dihedral
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angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
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restraint coefficient. The fourth example applies similar restraints
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to multiple dihedral angles using a restraint coefficient that
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increases from 0.0 to 2000.0 over the course of the run.
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</P>
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@ -75,7 +77,7 @@ self-consistent minimization problem (see below).
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</P>
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<P>In order for a restraint to be effective, the restraint force must
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typically be significantly larger than the forces associated with
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conventional forcefield terms. If the restraint is applied during a
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conventional forcefield terms. If the restraint is applied during a
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dynamics run (as opposed to during an energy minimization), a large
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restraint coefficient can significantly reduce the stable timestep
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size, especially if the atoms are initially far from the preferred
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@ -85,17 +87,17 @@ works best for a given application.
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<P>For the case of finding a minimum energy structure for a single
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molecule with particular restratins (e.g. for fitting forcefield
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parameters or constructing a potential energy surface), commands such
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as the following might be useful:
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as the following may be useful:
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</P>
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<PRE># minimize molecule energy with restraints
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velocity all create 600.0 8675309 mom yes rot yes dist gaussian
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fix NVE all nve
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fix TFIX all langevin 600.0 0.0 100 24601
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fix REST all restrain 0.0 5000.0 dihedral 2 1 3 8 $<I>angle1</I> 3 1 2 9 $<I>angle2</I>
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fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $<I>angle1</I> dihedral 3 1 2 9 0.0 5000.0 $<I>angle2</I>
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fix_modify REST energy yes
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run 10000
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fix TFIX all langevin 0.0 0.0 100 24601
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fix REST all restrain 5000.0 5000.0 dihedral 2 1 3 8 $<I>angle1</I> 3 1 2 9 $<I>angle2</I>
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fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $<I>angle1</I> dihedral 3 1 2 9 5000.0 5000.0 $<I>angle2</I>
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fix_modify REST energy yes
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run 10000
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# sanity check for convergence
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@ -106,19 +108,57 @@ run 0
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</PRE>
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<HR>
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<P>The <I>bond</I> keyword applies a bond restraint to the specified atoms
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using the same functional form used by the <A HREF = "bond_harmonic.html">bond_style
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harmonic</A> command. The potential associated with
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the restraint is
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</P>
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<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
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</CENTER>
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<P>with the following coefficients:
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</P>
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<UL><LI>K (energy/distance^2)
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<LI>r0 (distance)
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</UL>
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<P>K and r0 are specified with the fix. Note that the usual 1/2 factor
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is included in K.
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</P>
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<HR>
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<P>The <I>angle</I> keyword applies an angle restraint to the specified atoms
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using the same functional form used by the <A HREF = "angle_harmonic.html">angle_style
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harmonic</A> command. The potential associated with
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the restraint is
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</P>
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<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
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</CENTER>
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<P>with the following coefficients:
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</P>
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<UL><LI>K (energy/radian^2)
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<LI>theta0 (degrees)
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</UL>
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<P>K and theta0 are specified with the fix. Note that the usual 1/2
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factor is included in K.
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</P>
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<HR>
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<P>The <I>dihedral</I> keyword applies a dihedral restraint to the specified
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atoms using a simplified form of the function used in <A HREF = "dihedral_charmm.html">dihedral_style
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charmm</A>. Specifically, the potential associated
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with the restraint is
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atoms using a simplified form of the function used by the
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<A HREF = "dihedral_charmm.html">dihedral_style charmm</A> command. The potential
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associated with the restraint is
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</P>
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<CENTER><IMG SRC = "Eqs/dihedral_charmm.jpg">
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</CENTER>
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<P>with the following coefficients:
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</P>
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<UL><LI>K (energy) = K (specified above)
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<UL><LI>K (energy)
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<LI>n = 1
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<LI>d (degrees) = 180.0 + target (specified above)
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<LI>d (degrees) = phi0 + 180
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</UL>
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<P>K and phi0 are specified with the fix. Note that the value of n is
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hard-wired to 1. Also note that the energy will be a minimum when the
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current dihedral angle phi is equal to phi0.
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</P>
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<HR>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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@ -138,18 +178,13 @@ the system (the quantity being minimized), you MUST enable the
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</P>
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<P>This fix computes a global scalar, which can be accessed by various
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<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
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potential energy discussed above. The scalar value calculated by this
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fix is "extensive".
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potential energy for all the restraints as discussed above. The scalar
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value calculated by this fix is "extensive".
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The group-ID specified by this fix is ignored.
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</P>
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<P>Currently, only dihedral restraints are allowed, but modification of
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the code to allow angle and bond restraints would be straightforward.
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B> none
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</P>
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@ -19,15 +19,15 @@ keyword = {bond} or {angle} or {dihedral} :l
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{bond} args = atom1 atom2 Kstart Kstop r0
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atom1,atom2 = IDs of 2 atoms in bond
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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r0 = target value for bond distance (distance units)
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{angle} args = atom1 atom2 atom3 Kstart Kstop theta
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r0 = equilibrium bond distance (distance units)
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{angle} args = atom1 atom2 atom3 Kstart Kstop theta0
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atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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theta = target value for angle theta (degrees)
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{bond} args = atom1 atom2 atom3 atom4 Kstart Kstop phi
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theta0 = equilibrium angle theta (degrees)
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{bond} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
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atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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phi = target value for dihedral angle phi (degrees) :pre
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phi0 = equilibrium dihedral angle phi (degrees) :pre
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:ule
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[Examples:]
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@ -40,20 +40,22 @@ fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5
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[Description:]
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Restrain the motion of the specified sets of atoms by making them part
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of bond or angle or dihedral interaction whose strength can vary over
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time during a simulation. This is functionally equivalent to creating
|
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a bond or angle or dihedral for the same atoms in a data file, as
|
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specified by the "read_data"_read_data.html command, albeit with a
|
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time-varying pre-factor coefficient. For the purpose of forcefield
|
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parameter-fitting or mapping a molecular potential energy surface,
|
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this fix reduces the hassle and risk associated with modifying data
|
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files. In other words, use this fix to temporarily force a molecule
|
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to adopt a particular conformation. To create a permanent bond or
|
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angle or dihedral, you should modify the data file.
|
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of a bond or angle or dihedral interaction whose strength can vary
|
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over time during a simulation. This is functionally equivalent to
|
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creating a bond or angle or dihedral for the same atoms in a data
|
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file, as specified by the "read_data"_read_data.html command, albeit
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with a time-varying pre-factor coefficient. For the purpose of
|
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forcefield parameter-fitting or mapping a molecular potential energy
|
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surface, this fix reduces the hassle and risk associated with
|
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modifying data files. In other words, use this fix to temporarily
|
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force a molecule to adopt a particular conformation. To create a
|
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permanent bond or angle or dihedral, you should modify the data file.
|
||||
|
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The first example above applies a restraint to hold the dihedral angle
|
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formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
|
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restraint coefficient. The second example applies similar restraints
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The group-ID specified by this fix is ignored.
|
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The second example above applies a restraint to hold the dihedral
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angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
|
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restraint coefficient. The fourth example applies similar restraints
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to multiple dihedral angles using a restraint coefficient that
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increases from 0.0 to 2000.0 over the course of the run.
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@ -67,7 +69,7 @@ self-consistent minimization problem (see below).
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In order for a restraint to be effective, the restraint force must
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typically be significantly larger than the forces associated with
|
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conventional forcefield terms. If the restraint is applied during a
|
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conventional forcefield terms. If the restraint is applied during a
|
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dynamics run (as opposed to during an energy minimization), a large
|
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restraint coefficient can significantly reduce the stable timestep
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size, especially if the atoms are initially far from the preferred
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@ -77,17 +79,17 @@ works best for a given application.
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For the case of finding a minimum energy structure for a single
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molecule with particular restratins (e.g. for fitting forcefield
|
||||
parameters or constructing a potential energy surface), commands such
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||||
as the following might be useful:
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||||
as the following may be useful:
|
||||
|
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# minimize molecule energy with restraints
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velocity all create 600.0 8675309 mom yes rot yes dist gaussian
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fix NVE all nve
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fix TFIX all langevin 600.0 0.0 100 24601
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fix REST all restrain 0.0 5000.0 dihedral 2 1 3 8 ${angle1} 3 1 2 9 ${angle2}
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fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2}
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fix_modify REST energy yes
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run 10000
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fix TFIX all langevin 0.0 0.0 100 24601
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fix REST all restrain 5000.0 5000.0 dihedral 2 1 3 8 ${angle1} 3 1 2 9 ${angle2}
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fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${angle2}
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fix_modify REST energy yes
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run 10000
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# sanity check for convergence
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@ -98,18 +100,56 @@ run 0 :pre
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:line
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The {bond} keyword applies a bond restraint to the specified atoms
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using the same functional form used by the "bond_style
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harmonic"_bond_harmonic.html command. The potential associated with
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the restraint is
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:c,image(Eqs/bond_harmonic.jpg)
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with the following coefficients:
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K (energy/distance^2)
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r0 (distance) :ul
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K and r0 are specified with the fix. Note that the usual 1/2 factor
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is included in K.
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:line
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The {angle} keyword applies an angle restraint to the specified atoms
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using the same functional form used by the "angle_style
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harmonic"_angle_harmonic.html command. The potential associated with
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the restraint is
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:c,image(Eqs/angle_harmonic.jpg)
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with the following coefficients:
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K (energy/radian^2)
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theta0 (degrees) :ul
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K and theta0 are specified with the fix. Note that the usual 1/2
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factor is included in K.
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:line
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The {dihedral} keyword applies a dihedral restraint to the specified
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atoms using a simplified form of the function used in "dihedral_style
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charmm"_dihedral_charmm.html. Specifically, the potential associated
|
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with the restraint is
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atoms using a simplified form of the function used by the
|
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"dihedral_style charmm"_dihedral_charmm.html command. The potential
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associated with the restraint is
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:c,image(Eqs/dihedral_charmm.jpg)
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with the following coefficients:
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K (energy) = K (specified above)
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K (energy)
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n = 1
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d (degrees) = 180.0 + target (specified above) :ul
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d (degrees) = phi0 + 180 :ul
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K and phi0 are specified with the fix. Note that the value of n is
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hard-wired to 1. Also note that the energy will be a minimum when the
|
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current dihedral angle phi is equal to phi0.
|
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|
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:line
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@ -130,18 +170,13 @@ the system (the quantity being minimized), you MUST enable the
|
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|
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This fix computes a global scalar, which can be accessed by various
|
||||
"output commands"_Section_howto.html#howto_15. The scalar is the
|
||||
potential energy discussed above. The scalar value calculated by this
|
||||
fix is "extensive".
|
||||
potential energy for all the restraints as discussed above. The scalar
|
||||
value calculated by this fix is "extensive".
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The group-ID specified by this fix is ignored.
|
||||
|
||||
Currently, only dihedral restraints are allowed, but modification of
|
||||
the code to allow angle and bond restraints would be straightforward.
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
|
||||
Reference in New Issue
Block a user