and the flexible constraints.</dd>
<dt><b>fcstep: (0) [ps<sup>2</sup>]</b></dt>
<dd>the step size for optimizing the flexible constraints.
-Should be chosen as mu/(d<sup>2</sup>V/d q<sup>2</sup>)
+Should be chosen as mu/(d<sup>2</sup>V/dq<sup>2</sup>)
where mu is the reduced mass of two particles in a flexible constraint
-and d<sup>2</sup>V/d q<sup>2</sup> is the second derivative of the potential
+and d<sup>2</sup>V/dq<sup>2</sup> is the second derivative of the potential
in the constraint direction. Hopefully this number does not differ too
much between the flexible constraints, as the number of iterations
and thus the runtime is very sensitive to <tt>fcstep</tt>.
<dd><dl compact>
<dt><b>>0</b></dt>
<dd>Frequency to update the <!--Idx-->neighbor list<!--EIdx--> (and
-the long-range forces, when using twin-range cut-off's). When this is 0,
+the long-range forces, when using twin-range cut-offs). When this is 0,
the neighbor list is made only once.
With energy minimization the neighborlist will be updated for every
energy evaluation when <b>nstlist</b><tt>>0</tt>.</dd>
<dd><dl compact>
<dt><b>Cut-off</b></dt>
-<dd>Twin range cut-off's with neighborlist cut-off <b>rlist</b> and
+<dd>Twin range cut-offs with neighborlist cut-off <b>rlist</b> and
Coulomb cut-off <b>rcoulomb</b>,
where <b>rcoulomb</b>≥<b>rlist</b>.
<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 ionic strength is computed from the number of charged
(i.e. with non zero charge) <!--Idx-->charge group<!--EIdx-->s.
<tt>f(x)</tt>, <tt>-f'(x)</tt>,
<tt>g(x)</tt>, <tt>-g'(x)</tt>,
<tt>h(x)</tt>, <tt>-h'(x)</tt>,
-where f(x) is the Coulomb function, g(x) the dispersion function
-and h(x) the repulsion function.
+where <tt>f(x)</tt> is the Coulomb function, <tt>g(x)</tt> the dispersion function
+and <tt>h(x)</tt> the repulsion function.
When <b>vdwtype</b> is not set to <b>User</b> the values
-for g, -g', h and -h' are ignored.
+for <tt>g</tt>, <tt>-g'</tt>, <tt>h</tt> and <tt>-h'</tt> are ignored.
For the non-bonded interactions <tt>x</tt> values should run
from 0 to the largest cut-off distance + <b>table-extension</b>
and should be uniformly spaced. For the pair interactions the table
<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>
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>
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>.
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
<dt><b>3d</b></dt>
<dd>The Ewald sum is performed in all three dimensions.</dd>
<dt><b>3dc</b></dt>
-<dd>The reciprocal sum is still performed in 3d,
-but a force and potential correction applied in the z
-dimension to produce a pseudo-2d summation.
-If your system has a slab geometry in the x-y plane you can
-try to increase the z-dimension of the box (a box height of 3 times
+<dd>The reciprocal sum is still performed in 3D,
+but a force and potential correction applied in the <tt>z</tt>
+dimension to produce a pseudo-2D summation.
+If your system has a slab geometry in the <tt>x-y</tt> plane you can
+try to increase the <tt>z</tt>-dimension of the box (a box height of 3 times
the slab height is usually ok)
and use this option.</dd>
</dl></dd>
<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.
<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 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>.
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>.
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>
<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
<dd>Do a QM/MM simulation. Several groups can be described at
different QM levels separately. These are specified in
the <b>QMMM-grps</b> field separated by spaces. The level of <i>ab
-initio</i> theory at which the groups are described is speficied
+initio</i> theory at which the groups are described is specified
by <b>QMmethod</b> and <b>QMbasis</b> Fields. Describing the
groups at different levels of theory is only possible with the ONIOM
QM/MM scheme, specified by <b>QMMMscheme</b>.</dd>
and <b>CASorbitals</b>. </dd>
<dt><b>QMbasis: (STO-3G)</b></dt>
-<dd>Basisset used to expand the electronic wavefuntion. Only gaussian
-bassisets are currently available, <i>i.e.</i> STO-3G, 3-21G, 3-21G*,
+<dd>Basis set used to expand the electronic wavefuntion. Only Gaussian
+basis sets are currently available, <i>i.e.</i> STO-3G, 3-21G, 3-21G*,
3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*, and 6-311G.</dd>
<dt><b>QMcharge: (0) [integer]</b></dt>
-<dd>The total charge in <i>e</i> of the <b>QMMM-grps</b>. In case
+<dd>The total charge in <tt>e</tt> of the <b>QMMM-grps</b>. In case
there are more than one <b>QMMM-grps</b>, the total charge of each
ONIOM layer needs to be specified separately.</dd>
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff