2006-09-22 00:22:34 +08:00
|
|
|
<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>
|
2007-10-11 06:28:11 +08:00
|
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
2007-06-26 08:03:39 +08:00
|
|
|
</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
|
2007-10-11 06:28:11 +08:00
|
|
|
are relevant to this fix. No global scalar or vector or per-atom
|
|
|
|
|
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
|
|
|
|
|
commands</A>. 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>.
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<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>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
