forked from lijiext/lammps
163 lines
6.9 KiB
HTML
163 lines
6.9 KiB
HTML
<HTML>
|
|
<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>
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
<H3>fix smd command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>fix ID group-ID smd type values keyword values
|
|
</PRE>
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
<LI>smd = style name of this fix command
|
|
|
|
<LI>mode = <I>cvel</I> or <I>cfor</I> to select constant velocity or constant force SMD
|
|
|
|
<PRE> <I>cvel</I> values = K vel
|
|
K = spring constant (force/distance units)
|
|
vel = velocity of pulling (distance/time units)
|
|
<I>cfor</I> values = force
|
|
force = pulling force (force units)
|
|
</PRE>
|
|
<LI>keyword = <I>tether</I> or <I>couple</I>
|
|
|
|
<PRE> <I>tether</I> values = x y z R0
|
|
x,y,z = point to which spring is tethered
|
|
R0 = distance of end of spring from tether point (distance units)
|
|
<I>couple</I> values = group-ID2 x y z R0
|
|
group-ID2 = 2nd group to couple to fix group with a spring
|
|
x,y,z = direction of spring, automatically computed with 'auto'
|
|
R0 = distance of end of spring (distance units)
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
|
|
fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
|
|
fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0
|
|
fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>This fix implements several options of steered MD (SMD) as reviewed in
|
|
<A HREF = "#Izrailev">(Izrailev)</A>, which allows to induce conformational changes
|
|
in systems and to compute the potential of mean force (PMF) along the
|
|
assumed reaction coordinate <A HREF = "#Park">(Park)</A> based on Jarzynski's
|
|
equality <A HREF = "#Jarzynski">(Jarzynski)</A>. This fix borrows a lot from <A HREF = "fix_spring.html">fix
|
|
spring</A> and <A HREF = "fix_setforce.html">fix setforce</A>.
|
|
</P>
|
|
<P>You can apply a moving spring force to a group of atoms (<I>tether</I>
|
|
style) or between two groups of atoms (<I>couple</I> style). The spring
|
|
can then be used in either constant velocity (<I>cvel</I>) mode or in
|
|
constant force (<I>cfor</I>) mode to induce transitions in your systems.
|
|
When running in <I>tether</I> style, you may need some way to fix some
|
|
other part of the system (e.g. via <A HREF = "fix_spring_self.html">fix
|
|
spring/self</A>)
|
|
</P>
|
|
<P>The <I>tether</I> style attaches a spring between a point at a distance of
|
|
R0 away from a fixed point <I>x,y,z</I> and the center of mass of the fix
|
|
group of atoms. A restoring force of magnitude K (R - R0) Mi / M is
|
|
applied to each atom in the group where <I>K</I> is the spring constant, Mi
|
|
is the mass of the atom, and M is the total mass of all atoms in the
|
|
group. Note that <I>K</I> thus represents the total force on the group of
|
|
atoms, not a per-atom force.
|
|
</P>
|
|
<P>In <I>cvel</I> mode the distance R is incremented or decremented
|
|
monotonously according to the pulling (or pushing) velocity.
|
|
In <I>cfor</I> mode a constant force is added and the actual distance
|
|
in direction of the spring is recorded.
|
|
</P>
|
|
<P>The <I>couple</I> style links two groups of atoms together. The first
|
|
group is the fix group; the second is specified by group-ID2. The
|
|
groups are coupled together by a spring that is at equilibrium when
|
|
the two groups are displaced by a vector in direction <I>x,y,z</I> with
|
|
respect to each other and at a distance R0 from that displacement.
|
|
Note that <I>x,y,z</I> only provides a direction and will be internally
|
|
normalized. But since it represents the <I>absolute</I> displacement of
|
|
group-ID2 relative to the fix group, (1,1,0) is a different spring
|
|
than (-1,-1,0). For each vector component, the displacement can be
|
|
described with the <I>auto</I> parameter. In this case the direction is
|
|
recomputed in every step, which can be useful for steering a local
|
|
process where the whole object undergoes some other change. When the
|
|
relative positions and distance between the two groups are not in
|
|
equilibrium, the same spring force described above is applied to atoms
|
|
in each of the two groups.
|
|
</P>
|
|
<P>For both the <I>tether</I> and <I>couple</I> styles, any of the x,y,z values can
|
|
be specified as NULL which means do not include that dimension in the
|
|
distance calculation or force application.
|
|
</P>
|
|
<P>For constant velocity pulling (<I>cvel</I> mode), the running integral
|
|
over the pulling force in direction of the spring is recorded and
|
|
can then later be used to compute the potential of mean force (PMF)
|
|
by averaging over multiple independent trajectories along the same
|
|
pulling path.
|
|
</P>
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
|
</P>
|
|
<P>The fix stores the direction of the spring, current pulling target
|
|
distance and the running PMF to <A HREF = "restart.html">binary restart files</A>.
|
|
See the <A HREF = "read_restart.html">read_restart</A> command for info on how to
|
|
re-specify a fix in an input script that reads a restart file, so that
|
|
the operation of the fix continues in an uninterrupted fashion.
|
|
</P>
|
|
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
|
|
fix.
|
|
</P>
|
|
<P>This fix computes a vector list of 7 quantities, which can be accessed
|
|
by various <A HREF = "Section_howto.html#4_15">output commands</A>. The quantities
|
|
in the vector are in this order: the x-, y-, and z-component of the
|
|
pulling force, the total force in direction of the pull, the
|
|
equilibrium distance of the spring, the distance between the two
|
|
reference points, and finally the accumulated PMF (the sum of pulling
|
|
forces times displacement).
|
|
</P>
|
|
<P>The force is the total force on the group of atoms by the spring. In
|
|
the case of the <I>couple</I> style, it is the force on the fix group
|
|
(group-ID) or the negative of the force on the 2nd group (group-ID2).
|
|
The vector values calculated by this fix are "extensive".
|
|
</P>
|
|
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
|
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
|
minimization</A>.
|
|
</P>
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>This fix is part of the "user-misc" package. It is only enabled if
|
|
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
|
LAMMPS</A> section for more info.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "fix_drag.html">fix drag</A>, <A HREF = "fix_spring.html">fix spring</A>,
|
|
<A HREF = "fix_spring_self.html">fix spring/self</A>,
|
|
<A HREF = "fix_spring_rg.html">fix spring/rg</A>
|
|
</P>
|
|
<P><B>Default:</B> none
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "Israilev"></A>
|
|
|
|
<P><B>(Izrailev)</B> Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
|
|
Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
|
|
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
|
|
Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
|
|
</P>
|
|
<P><B>(Park)</B>
|
|
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
|
|
</P>
|
|
<P><B>(Jarzynski)</B>
|
|
Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
|
|
</P>
|
|
</HTML>
|