<dt><b>Generalized-Reaction-Field</b></dt>
<dd>Generalized reaction field with Coulomb cut-off <b>rcoulomb</b>,
- where <b>rcoulomb</b> &ge <b>rlist</b>.
+ where <b>rcoulomb</b> ≥ <b>rlist</b>.
-The dielectric constant beyond the cut-off is <b>epsilon_rf</b>.
+The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
The ionic strength is computed from the number of charged
(i.e. with non zero charge) <!--Idx-->charge group<!--EIdx-->s.
The temperature for the GRF potential is set with
<dt><b>vdwtype:</b></dt>
<dd><dl compact>
<dt><b>Cut-off</b></dt>
- <dd>Twin range cut-off's with neighbor list cut-off <b>rlist</b> and
+ <dd>Twin range cut-offs with neighbor list cut-off <b>rlist</b> and
VdW cut-off <b>rvdw</b>,
- where <b>rvdw</b> <tt>&ge</tt> <b>rlist</b>.</dd>
+ where <b>rvdw</b> <tt>≥</tt> <b>rlist</b>.</dd>
<dt><b>Shift</b></dt>
<dd>The LJ (not Buckingham) potential is decreased over the whole
-range and the forces decay smoothly to zero between <b>rvdw_switch</b>
+range and the forces decay smoothly to zero between <b>rvdw-switch</b>
and <b>rvdw</b>. The neighbor search cut-off <b>rlist</b> should be
0.1 to 0.3 nm larger than <b>rvdw</b> to accommodate for the size of
charge groups and diffusion between neighbor list
use LJ correction, make sure that <b>rvdw</b> corresponds to the
cut-off in the user-defined function.
When <b>coulombtype</b> is not set to <b>User</b> the values
- for f and -f' are ignored.</dd>
+ for <tt>f</tt> and <tt>-f'</tt> are ignored.</dd>
</dl></dd>
-<dt><b>rvdw_switch: (0) [nm]</b></dt>
+<dt><b>rvdw-switch: (0) [nm]</b></dt>
<dd>where to start switching the LJ potential</dd>
<dt><b>rvdw: (1) [nm]</b></dt>
For ordinary Ewald the spacing times the box dimensions determines the
highest magnitude to use in each direction. In all cases
each direction can be overridden by entering a non-zero value for
- <b>fourier-n*</b>.
-<b>fourier_n[xyz]</b>.
++<b>fourier-n[xyz]</b>.
For optimizing the relative load of the particle-particle interactions
and the mesh part of PME it is useful to know that
the accuracy of the electrostatics remains nearly constant
and use this option.</dd>
</dl></dd>
-<dt><b>epsilon_surface: (0)</b></dt>
+<dt><b>epsilon-surface: (0)</b></dt>
- <dd>This controls the dipole correction to the Ewald summation in 3d. The
+ <dd>This controls the dipole correction to the Ewald summation in 3D. The
default value of zero means it is turned off. Turn it on by setting it to the value
of the relative permittivity of the imaginary surface around your infinite system. Be
careful - you shouldn't use this if you have free mobile charges in your system.
<dt><b>pcoupltype:</b></dt>
<dd><dl compact>
<dt><b>isotropic</b></dt>
-<dd>Isotropic pressure coupling with time constant <b>tau_p</b> [ps].
+<dd>Isotropic pressure coupling with time constant <b>tau-p</b> [ps].
The compressibility and reference pressure are set with
-<b>compressibility</b> [bar<sup>-1</sup>] and <b>ref_p</b> [bar], one
+<b>compressibility</b> [bar<sup>-1</sup>] and <b>ref-p</b> [bar], one
value is needed.</dd>
<dt><b>semiisotropic</b></dt>
- <dd>Pressure coupling which is isotropic in the x and y direction,
- but different in the z direction.
+ <dd>Pressure coupling which is isotropic in the <tt>x</tt> and <tt>y</tt> direction,
+ but different in the <tt>z</tt> direction.
This can be useful for membrane simulations.
- 2 values are needed for x/y and z directions respectively.</dd>
+ 2 values are needed for <tt>x/y</tt> and <tt>z</tt> directions respectively.</dd>
<dt><b>anisotropic</b></dt>
- <dd>Idem, but 6 values are needed for xx, yy, zz, xy/yx, xz/zx and yz/zy
+ <dd>Idem, but 6 values are needed for <tt>xx</tt>, <tt>yy</tt>, <tt>zz</tt>, <tt>xy/yx</tt>, <tt>xz/zx</tt> and <tt>yz/zy</tt>
components, respectively.
When the off-diagonal compressibilities are set to zero,
a rectangular box will stay rectangular.
of the simulation box.</dd>
<dt><b>surface-tension</b></dt>
<dd>Surface tension coupling for surfaces parallel to the xy-plane.
- Uses normal pressure coupling for the z-direction, while the surface tension
- is coupled to the x/y dimensions of the box.
+ Uses normal pressure coupling for the <tt>z</tt>-direction, while the surface tension
+ is coupled to the <tt>x/y</tt> dimensions of the box.
-The first <b>ref_p</b> value is the reference surface tension times
+The first <b>ref-p</b> value is the reference surface tension times
the number of surfaces [bar nm],
- the second value is the reference z-pressure [bar].
+ the second value is the reference <tt>z</tt>-pressure [bar].
The two <b>compressibility</b> [bar<sup>-1</sup>] values are the compressibility
- in the x/y and z direction respectively.
- The value for the z-compressibility should be reasonably accurate since it
+ in the <tt>x/y</tt> and <tt>z</tt> direction respectively.
+ The value for the <tt>z</tt>-compressibility should be reasonably accurate since it
influences the convergence of the surface-tension, it can also be set to zero
to have a box with constant height.</dd>
</dl></dd>
<h3><!--Idx-->Walls<!--EIdx--></h3>
<dl>
<dt><b>nwall: 0</b></dt>
- <dd>When set to <b>1</b> there is a wall at z=0, when set to <b>2</b>
- there is also a wall at z=z-box. Walls can only be used with <b>pbc=xy</b>.
+ <dd>When set to <b>1</b> there is a wall at <tt>z=0</tt>, when set to <b>2</b>
-there is also a wall at <tt>z=z_box</tt>. Walls can only be used with <b>pbc=xy</b>.
++there is also a wall at <tt>z=z-box</tt>. Walls can only be used with <b>pbc=xy</b>.
When set to <b>2</b> pressure coupling and Ewald summation can be used
(it is usually best to use semiisotropic pressure coupling with
- the x/y compressibility set to 0, as otherwise the surface area will change).
+ the <tt>x/y</tt> compressibility set to 0, as otherwise the surface area will change).
-Walls interact wit the rest of the system through an optional <tt>wall_atomtype</tt>.
+Walls interact wit the rest of the system through an optional <tt>wall-atomtype</tt>.
Energy groups <tt>wall0</tt> and <tt>wall1</tt> (for <b>nwall=2</b>) are
added automatically to monitor the interaction of energy groups
with each wall.
The <A HREF="#run">center of mass motion removal</A> will be turned
- off in the z-direction.</dd>
+ off in the <tt>z</tt>-direction.</dd>
-<dt><b>wall_atomtype:</b></dt>
+<dt><b>wall-atomtype:</b></dt>
<dd>the atom type name in the force field for each wall.
By (for example) defining a special wall atom type in the topology with its
own combination rules, this allows for independent tuning of the interaction
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