forked from lijiext/lammps
163 lines
7.0 KiB
HTML
163 lines
7.0 KiB
HTML
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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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<HR>
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<H3>fix smd 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 smd type values keyword values
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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>smd = style name of this fix command
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<LI>mode = <I>cvel</I> or <I>cfor</I> to select constant velocity or constant force SMD
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<LI> <I>cvel</I> values = K vel
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K = spring constant (force/distance units)
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vel = velocity of pulling (distance/time units)
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<I>cfor</I> values = force
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force = pulling force (force units)
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keyword = <I>tether</I> or <I>couple</I>
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<PRE> <I>tether</I> values = x y z R0
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x,y,z = point to which spring is tethered
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R0 = distance of end of spring from tether point (distance units)
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<I>couple</I> values = group-ID2 x y z R0
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group-ID2 = 2nd group to couple to fix group with a spring
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x,y,z = direction of spring, automatically computed with 'auto'
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R0 = distance of end of spring (distance units)
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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 pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
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fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
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fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0
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fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 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>This fix implements several options of steered MD (SMD) as reviewed in
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<A HREF = "#Izrailev">(Izrailev)</A>, which allows to induce conformational changes
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in systems and to compute the potential of mean force (PMF) along the
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assumed reaction coordinate <A HREF = "#Park">(Park)</A> based on Jarzynski's
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equality <A HREF = "#Jarzynski">(Jarzynski)</A>. This fix borrows a lot from <A HREF = "fix_spring.html">fix
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spring</A> and <A HREF = "fix_setforce.html">fix setforce</A>.
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</P>
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<P>You can apply a moving spring force to a group of atoms (<I>tether</I>
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style) or between two groups of atoms (<I>couple</I> style). The spring
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can then be used in either constant velocity (<I>cvel</I>) mode or in
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constant force (<I>cfor</I>) mode to induce transitions in your systems.
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When running in <I>tether</I> style, you may need some way to fix some
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other part of the system (e.g. via <A HREF = "fix_spring_self.html">fix
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spring/self</A>)
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</P>
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<P>The <I>tether</I> style attaches a spring between a point at a distance of
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R0 away from a fixed point <I>x,y,z</I> and the center of mass of the fix
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group of atoms. A restoring force of magnitude K (R - R0) Mi / M is
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applied to each atom in the group where <I>K</I> is the spring constant, Mi
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is the mass of the atom, and M is the total mass of all atoms in the
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group. Note that <I>K</I> thus represents the total force on the group of
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atoms, not a per-atom force.
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</P>
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<P>In <I>cvel</I> mode the distance R is incremented or decremented
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monotonously according to the pulling (or pushing) velocity.
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In <I>cfor</I> mode a constant force is added and the actual distance
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in direction of the spring is recorded.
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</P>
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<P>The <I>couple</I> style links two groups of atoms together. The first
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group is the fix group; the second is specified by group-ID2. The
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groups are coupled together by a spring that is at equilibrium when
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the two groups are displaced by a vector in direction <I>x,y,z</I> with
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respect to each other and at a distance R0 from that displacement.
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Note that <I>x,y,z</I> only provides a direction and will be internally
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normalized. But since it represents the <I>absolute</I> displacement of
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group-ID2 relative to the fix group, (1,1,0) is a different spring
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than (-1,-1,0). For each vector component, the displacement can be
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described with the <I>auto</I> parameter. In this case the direction is
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recomputed in every step, which can be useful for steering a local
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process where the whole object undergoes some other change. When the
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relative positions and distance between the two groups are not in
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equilibrium, the same spring force described above is applied to atoms
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in each of the two groups.
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</P>
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<P>For both the <I>tether</I> and <I>couple</I> styles, any of the x,y,z values can
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be specified as NULL which means do not include that dimension in the
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distance calculation or force application.
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</P>
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<P>For constant velocity pulling (<I>cvel</I> mode), the running integral
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over the pulling force in direction of the spring is recorded and
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can then later be used to compute the potential of mean force (PMF)
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by averaging over multiple independent trajectories along the same
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pulling path.
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</P>
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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>The fix stores the direction of the spring, current pulling target
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distance and the running PMF to <A HREF = "restart.html">binary restart files</A>.
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See the <A HREF = "read_restart.html">read_restart</A> command for info on how to
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re-specify a fix in an input script that reads a restart file, so that
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the operation of the fix continues in an uninterrupted fashion.
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</P>
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<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
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fix.
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</P>
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<P>This fix computes a vector list of 7 quantities, which can be accessed
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by various <A HREF = "Section_howto.html#4_15">output commands</A>. The quantities
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in the vector are in this order: the x-, y-, and z-component of the
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pulling force, the total force in direction of the pull, the
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equilibrium distance of the spring, the distance between the two
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reference points, and finally the accumulated PMF (the sum of pulling
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forces times displacement).
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</P>
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<P>The force is the total force on the group of atoms by the spring. In
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the case of the <I>couple</I> style, it is the force on the fix group
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(group-ID) or the negative of the force on the 2nd group (group-ID2).
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The vector values calculated by this fix are "extensive", meaning they
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scale with the number of atoms in the simulation.
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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. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This fix is part of the "user-smd" package. It is only enabled if
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LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_drag.html">fix drag</A>, <A HREF = "fix_spring.html">fix spring</A>,
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<A HREF = "fix_spring_self.html">fix spring/self</A>,
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<A HREF = "fix_spring_rg.html">fix spring/rg</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Israilev"></A>
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<P><B>(Izrailev)</B> Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
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Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
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Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
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Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
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</P>
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<P><B>(Park)</B>
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Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
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</P>
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<P><B>(Jarzynski)</B>
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Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
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</P>
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</HTML>
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