Various editorial and formatting fixes

diff --git a/share/html/online/mdp_opt.html b/share/html/online/mdp_opt.html
index 1ef2fe01064f73ab50a57394715c7b5f2d865dd0..444dac03bce8ff9d3968d4f831f608739cc2e20e 100644 (file)
--- a/share/html/online/mdp_opt.html
+++ b/share/html/online/mdp_opt.html
@@ -349,7 +349,7 @@ the last velocities are always written</dd>
 <dd>frequency to write energies to <!--Idx-->log file<!--EIdx-->,
 the last energies are always written</dd>
 <dt><b>nstcalcenergy: (-1)</b></dt>
-<dd>The frequency for calculating the energies, 0 is never.
+<dd>frequency for calculating the energies, 0 is never.
 This option is only relevant with dynamics.
 With a twin-range cut-off setup <b>nstcalcenergy</b> should be equal to
 or a multiple of <b>nstlist</b>.
@@ -364,8 +364,8 @@ the lowest common denominator of <b>nstenergy</b> and <b>nstlist</b> is used.
 <dt><b>nstenergy: (100) [steps]</b></dt>
 <dd>frequency to write energies to energy file,
 the last energies are always written,
-should be a multiple of <b>nstcalcenergy</b></dd>,
-note that the exact sums and fluctuations over all MD steps
+should be a multiple of <b>nstcalcenergy</b>.
+Note that the exact sums and fluctuations over all MD steps
 modulo <b>nstcalcenergy</b> are stored in the energy file,
 so <tt>g_energy</tt> can report exact
 energy averages and fluctuations also when <b>nstenergy</b><tt>&gt;1</tt></dd>
@@ -391,7 +391,7 @@ energy averages and fluctuations also when <b>nstenergy</b><tt>&gt;1</tt></dd>
 the long-range forces, when using twin-range cut-off's). 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>&gt;0</tt></dd>.
+energy evaluation when <b>nstlist</b><tt>&gt;0</tt>.</dd>
 <dt><b>0</b></dt>
 <dd>The neighbor list is only constructed once and never updated.
 This is mainly useful for vacuum simulations in which all particles
@@ -595,30 +595,24 @@ The function value at <tt>x=0</tt> is not important. More information is
 in the printed manual.</dd>
 
 <dt><b>PME-Switch</b></dt>
-<dd>
-A combination of PME and a switch function for the direct-space part
-(see above).
-<b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
+<dd>A combination of PME and a switch function for the direct-space part
+(see above). <b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
 This is mainly useful constant energy simulations. For constant temperature
 simulations the advantage of improved energy conservation
 is usually outweighed by the small loss in accuracy of the electrostatics.
 </dd>
 
 <dt><b>PME-User</b></dt>
-<dd>
-A combination of PME and user tables (see above).
+<dd>A combination of PME and user tables (see above).
 <b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
 The PME mesh contribution is subtracted from the user table by <tt>mdrun</tt>.
 Because of this subtraction the user tables should contain
-about 10 decimal places.
-</dd>
+about 10 decimal places.</dd>
 
 <dt><b>PME-User-Switch</b></dt>
-<dd>
-A combination of PME-User and a switching function (see above).
+<dd>A combination of PME-User and a switching function (see above).
 The switching function is applied to final particle-particle interaction,
-i.e. both to the user supplied function and the PME Mesh correction part.
-</dd>
+i.e. both to the user supplied function and the PME Mesh correction part.</dd>
 
 </dl></dd>
 
@@ -868,9 +862,9 @@ probably a better method when you want to apply pressure scaling
 during data collection, but beware that you can get very large
 oscillations if you are starting from a different pressure. For
 simulations where the exact fluctation of the NPT ensemble are
-important, or if the pressure coupling time is very short,it may not
+important, or if the pressure coupling time is very short it may not
 be appropriate, as the previous time step pressure is used in some
-steps of the gromacs implementation for the current time step pressure.</dd>
+steps of the GROMACS implementation for the current time step pressure.</dd>
 </dl></dd>
 <dt><b>MTTK</b></dt>
 <dd>Martyna-Tuckerman-Tobias-Klein implementation, only useable with <b>md-vv</b>
@@ -897,7 +891,7 @@ This can be useful for membrane simulations.
 2 values are needed for x/y and z 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
-components respectively.
+components, respectively.
 When the off-diagonal compressibilities are set to zero,
 a rectangular box will stay rectangular.
 Beware that anisotropic scaling can lead to extreme deformation
@@ -931,6 +925,7 @@ For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar<sup>-1</sup>].</
 <dt><b>ref_p: [bar]</b></dt>
 <dd>reference pressure for coupling</dd>
 <dt><b>refcoord_scaling:</b></dt>
+<dd><dl compact>
 <dt><b>no</b></dt>
 <dd>The reference coordinates for position restraints are not modified.
 Note that with this option the virial and pressure will depend on the absolute
@@ -939,6 +934,7 @@ positions of the reference coordinates.</dd>
 <dd>The reference coordinates are scaled with the scaling matrix of the pressure coupling.</dd>
 <dt><b>com</b></dt>
 <dd>Scale the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The vectors of each reference coordinate to the center of mass are not scaled. Only one COM is used, even when there are multiple molecules with position restraints. For calculating the COM of the reference coordinates in the starting configuration, periodic boundary conditions are not taken into account.
+</dl></dd>
 </dd>
 </dl>
 
@@ -1128,7 +1124,7 @@ 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 
 of each atomtype with the walls.</dd>
 <dt><b>wall_type:</b></dt>
-<dl>
+<dd><dl compact>
 <dt><b>9-3</b></dt>
 <dd>LJ integrated over the volume behind the wall: 9-3 potential</dd>
 <dt><b>10-4</b></dt>
@@ -1140,7 +1136,7 @@ the <b><A HREF="#table">energygrp_table</A></b> option,
 where the first name is for a ``normal'' energy group and the second name
 is <tt>wall0</tt> or <tt>wall1</tt>,
 only the dispersion and repulsion columns are used</dd>
-</dl>
+</dl></dd>
 <dt><b>wall_r_linpot: -1 (nm)</b></dt>
 <dd>Below this distance from the wall the potential is continued
 linearly and thus the force is constant. Setting this option to
@@ -1166,7 +1162,7 @@ interaction between periodic images.
 <h3>COM <!--Idx-->pulling<!--EIdx--></h3>
 <dl>
 <dt><b>pull:</b></dt>
-<dl>
+<dd><dl compact>
 <dt><b>no</b></dt>
 <dd>No center of mass pulling.
 All the following pull options will be ignored
@@ -1184,9 +1180,9 @@ that a rigid constraint is applied instead of a harmonic potential.</dd>
 a constant force. For this option there is no reference position
 and therefore the parameters <b>pull_init</b> and <b>pull_rate</b>
 are not used.</dd>
-</dl>
-<dt><b>pull_geometry</b></dt>
-<dl>
+</dl></dd>
+<dt><b>pull_geometry:</b></dt>
+<dd><dl compact>
 <dt><b>distance</b></dt>
 <dd>Pull along the vector connecting the two groups.
 Components can be selected with <b>pull_dim</b>.</dd>
@@ -1213,18 +1209,18 @@ from the COM of the pull group has both a radial and an axial component.
 <dt><b>position</b></dt>
 <dd>Pull to the position of the reference group plus
 <b>pull_init</b> + time*<b>pull_rate</b>*<b>pull_vec</b>.</dd>
-</dl>
+</dl></dd>
 <dt><b>pull_dim: (Y Y Y)</b></dt>
 <dd>the distance components to be used with geometry <b>distance</b>
-and <b>position</b></dd>, also sets which components are printed
-int the output files
+and <b>position</b>, and also sets which components are printed
+to the output files</dd>
 <dt><b>pull_r1: (1) [nm]</b></dt>
 <dd>the inner radius of the cylinder for geometry <b>cylinder</b></dd>
 <dt><b>pull_r0: (1) [nm]</b></dt>
 <dd>the outer radius of the cylinder for geometry <b>cylinder</b></dd>
 <dt><b>pull_constr_tol: (1e-6)</b></dt>
 <dd>the relative constraint tolerance for constraint pulling</dd>
-<dt><b>pull_start</b></dt>
+<dt><b>pull_start:</b></dt>
 <dd><dl compact>
 <dt><b>no</b></dt>
 <dd>do not modify <b>pull_init</b>
@@ -1435,14 +1431,14 @@ the molecule definition in the topology.</dd>
 <dt><b>nstdhdl: (10)</b></dt>
 <dd>the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg,
 0 means no ouput, should be a multiple of <b>nstcalcenergy</b></dd>
-<dt><b>separate_dhdl_file (yes)</b></dt>
+<dt><b>separate_dhdl_file: (yes)</b></dt>
 <dd><dl compact>
 <dt><b>yes</b></dt>
 <dd>the free energy values that are calculated (as specified with the <b>foreign-lambda</b> and <b>dhdl_derivatives</b> settings) are written out to a separate file, with the default name <tt>dhdl.xvg</tt>. This file can be used directly with <tt>g_bar</tt>.</dd>
 <dt><b>no</b></dt>
 <dd>The free energy values are written out to the energy output file (<tt>ener.edr</tt>, in accumulated blocks at every <b>nstenergy</b> steps), where they can be extracted with <tt>g_energy</tt> or used directly with <tt>g_bar</tt>.</dd>
 </dl>
-<dt><b>dh_hist_size (0)</b></dt>
+<dt><b>dh_hist_size: (0)</b></dt>
 <dd>If nonzero, specifies the size of the histogram into which the Delta H values (specified with <b>foreign_lambda</b>) and the derivative dH/dl values are binned, and written to ener.edr. This can be used to save disk space while calculating free energy differences. One histogram gets written for each <b>foreign lambda</b> and two for the dH/dl, at every <b>nstenergy</b> step. Be aware that incorrect histogram settings (too small size or too wide bins) can introduce errors. Do not use histograms unless you're certain you need it.</dd>
 <dt><b>dh_hist_spacing (0.1)</b></dt>
 <dd>Specifies the bin width of the histograms, in energy units. Used in conjunction with <b>dh_hist_size</b>. This size limits the accuracy with which free energies can be calculated.  Do not use histograms unless you're certain you need it.</dd>
@@ -1523,7 +1519,7 @@ since a cosine of frequency zero has no phase.</dd>
 <h3><!--Idx-->Mixed quantum/classical molecular dynamics<!--EIdx--></h3>
 
 <dl>
-<dt></dt><b>QMMM:</b>
+<dt><b>QMMM:</b></dt>
 <dd><dl compact="compact">
 <dt><b>no</b></dt>
 <dd>No QM/MM.</dd>
@@ -1537,10 +1533,10 @@ groups at different levels of theory is only possible with the ONIOM
 QM/MM scheme, specified by <b>QMMMscheme</b>.</dd>
 </dl></dd>
 
-<dt></dt><b>QMMM-grps:</b>
+<dt><b>QMMM-grps:</b></dt>
 <dd>groups to be descibed at the QM level</dd>
 
-<dt></dt><b>QMMMscheme:</b>
+<dt><b>QMMMscheme:</b></dt>
 <dd><dl compact="compact">
 <dt><b>normal</b></dt>
 <dd>normal QM/MM. There can only be one <b>QMMM-grps</b> that is modelled
@@ -1555,37 +1551,37 @@ method by Morokuma and co-workers. There can be more than one <b>QMMM-grps</b> e
 (<b>QMmethod</b> and <b>QMbasis</b>).
 </dd></dl></dd>
 
-<dt></dt><b>QMmethod: (RHF)</b>
+<dt><b>QMmethod: (RHF)</b></dt>
 <dd>Method used to compute the energy and gradients on the QM
 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
 included in the active space is specified by <b>CASelectrons</b>
 and <b>CASorbitals</b>. </dd>
 
-<dt></dt><b>QMbasis: (STO-3G)</b>
+<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*,
 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*, and 6-311G.</dd>
 
-<dt></dt><b>QMcharge: (0) [integer]</b>
+<dt><b>QMcharge: (0) [integer]</b></dt>
 <dd>The total charge in <i>e</i> 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>
 
-<dt></dt><b>QMmult: (1) [integer]</b>
+<dt><b>QMmult: (1) [integer]</b></dt>
 <dd>The multiplicity of the <b>QMMM-grps</b>. In case there are more
 than one <b>QMMM-grps</b>, the multiplicity of each ONIOM layer needs
 to be specified separately.</dd>
 
-<dt></dt><b>CASorbitals: (0) [integer]</b>
+<dt><b>CASorbitals: (0) [integer]</b></dt>
 <dd>The number of orbitals to be included in the active space when
 doing a CASSCF computation.</dd>
 
-<dt></dt><b>CASelectrons: (0) [integer]</b>
+<dt><b>CASelectrons: (0) [integer]</b></dt>
 <dd>The number of electrons to be included in the active space when
 doing a CASSCF computation.</dd>
 
-<dt></dt><b>SH:</b>
+<dt><b>SH:</b></dt>
 <dd><dl compact="compact">
 <dt><b>no</b></dt>
 <dd>No surface hopping. The system is always in the electronic
@@ -1604,7 +1600,7 @@ method.</dd>
 <h3>Implicit solvent</h3>
 
 <dl>
-<dt></dt><b>implicit_solvent:</b>
+<dt><b>implicit_solvent:</b></dt>
 <dd><dl compact="compact">
 <dt><b>no</b></dt>
 <dd>No implicit solvent</dd>
@@ -1615,7 +1611,7 @@ OBC. These are specified with the <b>gb_algorithm</b> field. The non-polar solva
 is specified with the <b>sa_algorithm</b> field.</dd>
 </dl>
 
-<dt></dt><b>gb_algorithm:</b>
+<dt><b>gb_algorithm:</b></dt>
 <dd><dl compact="compact">
 <dt><b>Still</b></dt>
 <dd>Use the Still method to calculate the Born radii</dd>
@@ -1625,30 +1621,30 @@ is specified with the <b>sa_algorithm</b> field.</dd>
 <dd>Use the Onufriev-Bashford-Case method to calculate the Born radii</dd>
 </dl>
 
-<dt></dt><b>nstgbradii: (1) [steps]</b>
+<dt><b>nstgbradii: (1) [steps]</b></dt>
 <dd>Frequency to (re)-calculate the Born radii. For most practial purposes,
 setting a value larger than 1 violates energy conservation and leads to
 unstable trajectories.</dd>
 
-<dt></dt><b>rgbradii: (1.0) [nm]</b>
+<dt><b>rgbradii: (1.0) [nm]</b></dt>
 <dd>Cut-off for the calculation of the Born radii. Currently must be equal to rlist</dd>
 
-<dt></dt><b>gb_epsilon_solvent: (80)</b>
+<dt><b>gb_epsilon_solvent: (80)</b></dt>
 <dd>Dielectric constant for the implicit solvent</dd>
 
-<dt></dt><b>gb_saltconc: (0) [M]</b>
+<dt><b>gb_saltconc: (0) [M]</b></dt>
 <dd>Salt concentration for implicit solvent models, currently not used</dd>
 
-<dt></dt><b>gb_obc_alpha (1); gb_obc_beta (0.8); gb_obc_gamma (4.85);</b>
+<dt><b>gb_obc_alpha (1); gb_obc_beta (0.8); gb_obc_gamma (4.85);</b></dt>
 <dd>Scale factors for the OBC model. Default values are OBC(II).
 Values for OBC(I) are 0.8, 0 and 2.91 respectively</dd>
 
-<dt></dt><b>gb_dielectric_offset: (0.009) [nm]</b>
+<dt><b>gb_dielectric_offset: (0.009) [nm]</b></dt>
 <dd>Distance for the di-electric offset when calculating the Born radii. This is
 the offset between the center of each atom the center of the polarization energy 
 for the corresponding atom</dd>
 
-<dt></dt><b>sa_algorithm</b>
+<dt><b>sa_algorithm</b></dt>
 <dd><dl compact="compact">
 <dt><b>Ace-approximation</b></dt>
 <dd>Use an Ace-type approximation (default)</dd>
@@ -1657,13 +1653,14 @@ for the corresponding atom</dd>
 calculated</dd>
 </dl>
 
-<dt></dt><b>sa_surface_tension: [kj/mol/nm2]</b>
-<dd>Default value for surface tension with SA algorithms. The default value is -1, 
-<br>Note that if this default value is not changed
-it will be over-ridden by grompp using values that are specific for the choice
-of radii algorithm (0.0049 kcal/mol/Angstrom2 for Still, 0.0054 kcal/mol/Angstrom2 
+<dt><b>sa_surface_tension: [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
+<dd>Default value for surface tension with SA algorithms. The default value is -1; 
+Note that if this default value is not changed
+it will be overridden by grompp using values that are specific for the choice
+of radii algorithm (0.0049 kcal/mol/Angstrom<sup>2</sup> for Still, 0.0054 kcal/mol/Angstrom<sup>2</sup> 
 for HCT/OBC)
-<br>Setting it to 0 will while using an sa_algorithm other than None means 
+
+Setting it to 0 will while using an sa_algorithm other than None means 
 no non-polar calculations are done.
 </dd>
 </dl>