forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6789 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
786bcba081
commit
0cc0882f08
|
|
@ -342,10 +342,11 @@ of each style or click on the style itself for a full description:
|
|||
<TR ALIGN="center"><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nph_sphere.html">nph/sphere</A></TD><TD ><A HREF = "fix_nh.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
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<TR ALIGN="center"><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
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</TD></TR></TABLE></DIV>
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<P>These are fix styles contributed by users, which can be used if
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|
|
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@ -451,6 +451,7 @@ of each style or click on the style itself for a full description:
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"qeq/comb"_fix_qeq_comb.html,
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"reax/bonds"_fix_reax_bonds.html,
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"recenter"_fix_recenter.html,
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"restrain"_fix_restrain.html,
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"rigid"_fix_rigid.html,
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"rigid/nve"_fix_rigid.html,
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"rigid/nvt"_fix_rigid.html,
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@ -211,6 +211,7 @@ list of fix styles available in LAMMPS:
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<LI><A HREF = "fix_press_berendsen.html">press/berendsen</A> - pressure control by Berendsen barostat
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<LI><A HREF = "fix_print.html">print</A> - print text and variables during a simulation
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<LI><A HREF = "fix_reax_bonds.html">reax/bonds</A> - write out ReaxFF bond information <A HREF = "fix_recenter.html">recenter</A> - constrain the center-of-mass position of a group of atoms
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<LI><A HREF = "fix_restrain.html">restrain</A> - constrain a bond, angle, dihedral
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<LI><A HREF = "fix_rigid.html">rigid</A> - constrain one or more clusters of atoms to move as a rigid body with NVE integration
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<LI><A HREF = "fix_rigid.html">rigid/nve</A> - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
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<LI><A HREF = "fix_rigid.html">rigid/nvt</A> - constrain one or more clusters of atoms to move as a rigid body with NVT integration
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@ -210,6 +210,7 @@ list of fix styles available in LAMMPS:
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"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \
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"recenter"_fix_recenter.html - constrain the center-of-mass position \
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of a group of atoms
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"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
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"rigid"_fix_rigid.html - constrain one or more clusters of atoms to \
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move as a rigid body with NVE integration
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"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to \
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|
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@ -0,0 +1,150 @@
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>fix restrain command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID restrain Kstart Kstop keyword value(s)
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>restrain = style name of this fix command
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<LI>Kstart, Kstop = restraint coefficient at start/end of run (energy
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units)
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<LI>one keyword with one or more sets of parameter values may be appended to args
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<LI>keyword = <I>dihedral</I>
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<PRE> <I>dihedral</I> value = atom1 atom2 atom3 atom4 target
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atom1,atom2,atom3,atom4 = IDs of 4 atoms in restrained dihedral
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target = target value for specified dihedral angle (degrees)
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix holdem all restrain 2000.0 2000.0 dihedral 1 2 3 4 120.0
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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
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Restrain the motion of the specified atoms by making them part of a
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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 atoms in a data file, as specified
|
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by the <A HREF = "read_data.html">read_data</A> command, albeit with a time-varying
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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
|
||||
files. In other words, use this fix to temporarily force a molecule
|
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to adopt a particular conformation. To form a permanent bond or angle
|
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or dihedral, 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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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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<P>IMPORTANT NOTE: Adding a force to atoms implies a change in their
|
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potential energy as they move due to the applied force field. For
|
||||
dynamics via the <A HREF = "run.html">run</A> command, this energy can be added to
|
||||
the system's potential energy for thermodynamic output (see below).
|
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For energy minimization via the <A HREF = "minimize.html">minimize</A> command, this
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energy must be added to the system's potential energy to formulate a
|
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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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dynamics run (as opposed to during an energy minimization), a large
|
||||
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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conformation. You may need to experiment to determine what value of K
|
||||
works best for a given application.
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</P>
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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
|
||||
parameters or constructing a potential energy surface), commands such
|
||||
as the following might 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_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_modify REST energy yes
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run 10000
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# sanity check for convergence
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minimize 1e-6 1e-9 1000 100000
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# report unrestrained energies
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unfix REST
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run 0
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</PRE>
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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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</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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<LI>n = 1
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<LI>d (degrees) = 180.0 + target (specified above)
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</UL>
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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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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
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fix to add the potential energy associated with this fix to the
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system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
|
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output</A>.
|
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</P>
|
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<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
|
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with the added forces to be included in the total potential energy of
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the system (the quantity being minimized), you MUST enable the
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<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
|
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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#4_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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</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.
|
||||
</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>
|
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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|
|
@ -0,0 +1,139 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
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|
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:line
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|
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fix restrain command :h3
|
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|
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[Syntax:]
|
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|
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fix ID group-ID restrain Kstart Kstop keyword value(s) :pre
|
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|
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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
|
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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
|
||||
:ule
|
||||
|
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[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
|
||||
|
||||
[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
|
||||
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
|
||||
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.
|
||||
|
||||
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
|
||||
to multiple dihedral angles using a restraint coefficient that
|
||||
increases from 0.0 to 2000.0 over the course of the run.
|
||||
|
||||
IMPORTANT NOTE: Adding a force to atoms implies a change in their
|
||||
potential energy as they move due to the applied force field. For
|
||||
dynamics via the "run"_run.html command, this energy can be added to
|
||||
the system's potential energy for thermodynamic output (see below).
|
||||
For energy minimization via the "minimize"_minimize.html command, this
|
||||
energy must be added to the system's potential energy to formulate a
|
||||
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
|
||||
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
|
||||
conformation. You may need to experiment to determine what value of K
|
||||
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:
|
||||
|
||||
# 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_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_modify REST energy yes
|
||||
run 10000
|
||||
# sanity check for convergence
|
||||
minimize 1e-6 1e-9 1000 100000
|
||||
# report unrestrained energies
|
||||
unfix REST
|
||||
run 0 :pre
|
||||
|
||||
:line
|
||||
|
||||
The {dihedral} keyword applies a dihedral restraint to the specified
|
||||
atoms using a simplified form of the function used in "dihedral_style
|
||||
charmm"_dihedral_charmm.html. Specifically, the potential associated
|
||||
with the restraint is
|
||||
|
||||
:c,image(Eqs/dihedral_charmm.jpg)
|
||||
|
||||
with the following coefficients:
|
||||
|
||||
K (energy) = K (specified above)
|
||||
n = 1
|
||||
d (degrees) = 180.0 + target (specified above) :ul
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the potential energy associated with this fix to the
|
||||
system's potential energy as part of "thermodynamic
|
||||
output"_thermo_style.html.
|
||||
|
||||
IMPORTANT NOTE: If you want the fictitious potential energy associated
|
||||
with the added forces to be included in the total potential energy of
|
||||
the system (the quantity being minimized), you MUST enable the
|
||||
"fix_modify"_fix_modify.html {energy} option for this fix.
|
||||
|
||||
This fix computes a global scalar, which can be accessed by various
|
||||
"output commands"_Section_howto.html#4_15. The scalar is the
|
||||
potential energy 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.
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
Loading…
Reference in New Issue