From 6416ae2ff1e4f318142b9fe5ee60c7b7da156bf0 Mon Sep 17 00:00:00 2001 From: Mark Abraham Date: Fri, 24 Feb 2012 11:29:21 +1100 Subject: [PATCH] Minor formatting fixes to .mdp option documentation Change-Id: I71762463880e4cb650f680a2ed83125e450f003a --- share/html/online/mdp_opt.html | 70 +++++++++++++++++++++--------------------- 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/share/html/online/mdp_opt.html b/share/html/online/mdp_opt.html index 4d4fbcd2d2..84c6bf37b8 100644 --- a/share/html/online/mdp_opt.html +++ b/share/html/online/mdp_opt.html @@ -315,9 +315,9 @@ variable is used for energy minimization as well the default is 10.0. and the flexible constraints.
fcstep: (0) [ps2]
the step size for optimizing the flexible constraints. -Should be chosen as mu/(d2V/d q2) +Should be chosen as mu/(d2V/dq2) where mu is the reduced mass of two particles in a flexible constraint -and d2V/d q2 is the second derivative of the potential +and d2V/dq2 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 fcstep. @@ -388,7 +388,7 @@ energy averages and fluctuations also when nstenergy>1
>0
Frequency to update the neighbor list (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 nstlist>0.
@@ -476,7 +476,7 @@ is automatically set to the longest cut-off distance.
Cut-off
-
Twin range cut-off's with neighborlist cut-off rlist and +
Twin range cut-offs with neighborlist cut-off rlist and Coulomb cut-off rcoulomb, where rcoulomb≥rlist. @@ -522,7 +522,7 @@ The dielectric constant can be set to infinity by setting epsilon_rf=
Generalized-Reaction-Field
Generalized reaction field with Coulomb cut-off rcoulomb, -where rcoulomb &ge rlist. +where rcoulomb ≥ rlist. The dielectric constant beyond the cut-off is epsilon_rf. The ionic strength is computed from the number of charged (i.e. with non zero charge) charge groups. @@ -580,10 +580,10 @@ columns: the x value, f(x), -f'(x), g(x), -g'(x), h(x), -h'(x), -where f(x) is the Coulomb function, g(x) the dispersion function -and h(x) the repulsion function. +where f(x) is the Coulomb function, g(x) the dispersion function +and h(x) the repulsion function. When vdwtype is not set to User the values -for g, -g', h and -h' are ignored. +for g, -g', h and -h' are ignored. For the non-bonded interactions x values should run from 0 to the largest cut-off distance + table-extension and should be uniformly spaced. For the pair interactions the table @@ -640,9 +640,9 @@ A value of 0 means infinity.
vdwtype:
Cut-off
-
Twin range cut-off's with neighbor list cut-off rlist and +
Twin range cut-offs with neighbor list cut-off rlist and VdW cut-off rvdw, -where rvdw &ge rlist.
+where rvdw ≥ rlist.
Shift
The LJ (not Buckingham) potential is decreased over the whole range and the forces decay smoothly to zero between rvdw_switch @@ -672,7 +672,7 @@ The function value at x=0 is not important. When you want to use LJ correction, make sure that rvdw corresponds to the cut-off in the user-defined function. When coulombtype is not set to User the values -for f and -f' are ignored.
+for f and -f' are ignored.
rvdw_switch: (0) [nm]
@@ -730,7 +730,7 @@ energy group pairs. 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 -fourier_n*. +fourier_n[xyz]. 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 @@ -758,17 +758,17 @@ but then you need more wave vectors for the reciprocal sum.
3d
The Ewald sum is performed in all three dimensions.
3dc
-
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 +
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 the slab height is usually ok) and use this option.
epsilon_surface: (0)
-
This controls the dipole correction to the Ewald summation in 3d. The +
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. @@ -885,12 +885,12 @@ The compressibility and reference pressure are set with compressibility [bar-1] and ref_p [bar], one value is needed.
semiisotropic
-
Pressure coupling which is isotropic in the x and y direction, -but different in the z direction. +
Pressure coupling which is isotropic in the x and y direction, +but different in the z direction. This can be useful for membrane simulations. -2 values are needed for x/y and z directions respectively.
+2 values are needed for x/y and z directions respectively.
anisotropic
-
Idem, but 6 values are needed for xx, yy, zz, xy/yx, xz/zx and yz/zy +
Idem, but 6 values are needed for xx, yy, zz, xy/yx, xz/zx and yz/zy components, respectively. When the off-diagonal compressibilities are set to zero, a rectangular box will stay rectangular. @@ -898,14 +898,14 @@ Beware that anisotropic scaling can lead to extreme deformation of the simulation box.
surface-tension
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 z-direction, while the surface tension +is coupled to the x/y dimensions of the box. The first ref_p 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 z-pressure [bar]. The two compressibility [bar-1] 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 x/y and z direction respectively. +The value for the z-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.
@@ -1107,17 +1107,17 @@ solvent. This is especially useful for speeding up energy calculations with

Walls

nwall: 0
-
When set to 1 there is a wall at z=0, when set to 2 -there is also a wall at z=z_box. Walls can only be used with pbc=xy. +
When set to 1 there is a wall at z=0, when set to 2 +there is also a wall at z=z_box. Walls can only be used with pbc=xy. When set to 2 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 x/y compressibility set to 0, as otherwise the surface area will change). Walls interact wit the rest of the system through an optional wall_atomtype. Energy groups wall0 and wall1 (for nwall=2) are added automatically to monitor the interaction of energy groups with each wall. The center of mass motion removal will be turned -off in the z-direction.
+off in the z-direction.
wall_atomtype:
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 @@ -1527,7 +1527,7 @@ since a cosine of frequency zero has no phase.
Do a QM/MM simulation. Several groups can be described at different QM levels separately. These are specified in the QMMM-grps field separated by spaces. The level of ab -initio theory at which the groups are described is speficied +initio theory at which the groups are described is specified by QMmethod and QMbasis Fields. Describing the groups at different levels of theory is only possible with the ONIOM QM/MM scheme, specified by QMMMscheme.
@@ -1559,12 +1559,12 @@ included in the active space is specified by CASelectrons and CASorbitals.
QMbasis: (STO-3G)
-
Basisset used to expand the electronic wavefuntion. Only gaussian -bassisets are currently available, i.e. STO-3G, 3-21G, 3-21G*, +
Basis set used to expand the electronic wavefuntion. Only Gaussian +basis sets are currently available, i.e. STO-3G, 3-21G, 3-21G*, 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*, and 6-311G.
QMcharge: (0) [integer]
-
The total charge in e of the QMMM-grps. In case +
The total charge in e of the QMMM-grps. In case there are more than one QMMM-grps, the total charge of each ONIOM layer needs to be specified separately.
-- 2.11.4.GIT