Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/fix_spring.html
50e0b2dacb81efficient_neuronet

Last Change
Raw File

fix_spring.html
View Options

<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 spring command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID spring keyword values
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>spring = style name of this fix command
<LI>keyword = <I>tether</I> or <I>couple</I>
<PRE> <I>tether</I> values = K x y z R0
K = spring constant (force/distance units)
x,y,z = point to which spring is tethered
R0 = equilibrium distance from tether point (distance units)
<I>couple</I> values = group-ID2 K x y z R0
group-ID2 = 2nd group to couple to fix group with a spring
K = spring constant (force/distance units)
x,y,z = direction of spring
R0 = equilibrium distance of spring (distance units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix pull ligand spring tether 50.0 0.0 0.0 0.0 0.0
fix pull ligand spring tether 50.0 0.0 0.0 0.0 5.0
fix pull ligand spring tether 50.0 NULL NULL 2.0 3.0
fix 5 bilayer1 spring couple bilayer2 100.0 NULL NULL 10.0 0.0
fix longitudinal pore spring couple ion 100.0 NULL NULL -20.0 0.0
fix radial pore spring couple ion 100.0 0.0 0.0 NULL 5.0
</PRE>
<P><B>Description:</B>
</P>
<P>Apply a spring force to a group of atoms or between two groups of
atoms. This is useful for applying an umbrella force to a small
molecule or lightly tethering a large group of atoms (e.g. all the
solvent or a large molecule) to the center of the simulation box so
that it doesn't wander away over the course of a long simulation. It
can also be used to hold the centers of mass of two groups of atoms at
a given distance or orientation with respect to each other.
</P>
<P>The <I>tether</I> style attaches a spring between a fixed point <I>x,y,z</I> and
the center of mass of the fix group of atoms. The equilibrium
position of the spring is R0. At each timestep the distance R from
the center of mass of the group of atoms to the tethering point is
computed, taking account of wrap-around in a periodic simulation box.
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>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 <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>
is the equilibrium displacement of group-ID2 relative to the fix
group. Thus (1,1,0) is a different spring than (-1,-1,0). 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>The first example above pulls the ligand towards the point (0,0,0).
The second example holds the ligand near the surface of a sphere of
radius 5 around the point (0,0,0). The third example holds the ligand
a distance 3 away from the z=2 plane (on either side).
</P>
<P>The fourth example holds 2 bilayers a distance 10 apart in z. For the
last two examples, imagine a pore (a slab of atoms with a cylindrical
hole cut out) oriented with the pore axis along z, and an ion moving
within the pore. The fifth example holds the ion a distance of -20
below the z = 0 center plane of the pore (umbrella sampling). The
last example holds the ion a distance 5 away from the pore axis
(assuming the center-of-mass of the pore in x,y is the pore axis).
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes a 3-vector of forces, which can be accessed by
various <A HREF = "Section_howto.html#4_15">output commands</A>. This 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", meaning they scale with the
number of atoms in the simulation.
</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> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_drag.html">fix drag</A>, <A HREF = "fix_spring_self.html">fix spring/self</A>,
<A HREF = "fix_spring_rg.html">fix spring/rg</A>, <A HREF = "fix_smd.html">fix smd</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
c4science · Help