From: Justin Lemkul Date: Mon, 17 Jan 2011 12:50:04 +0000 (-0500) Subject: Various editorial and formatting fixes X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=84b92f275135b0569a13fb05ce8cd5a1aa0e0c56;p=alexxy%2Fgromacs.git Various editorial and formatting fixes --- diff --git a/share/html/online/mdp_opt.html b/share/html/online/mdp_opt.html index 1ef2fe0106..444dac03bc 100644 --- a/share/html/online/mdp_opt.html +++ b/share/html/online/mdp_opt.html @@ -349,7 +349,7 @@ the last velocities are always written
frequency to write energies to log file, the last energies are always written
nstcalcenergy: (-1)
-
The frequency for calculating the energies, 0 is never. +
frequency for calculating the energies, 0 is never. This option is only relevant with dynamics. With a twin-range cut-off setup nstcalcenergy should be equal to or a multiple of nstlist. @@ -364,8 +364,8 @@ the lowest common denominator of nstenergy and nstlist is used.
nstenergy: (100) [steps]
frequency to write energies to energy file, the last energies are always written, -should be a multiple of nstcalcenergy
, -note that the exact sums and fluctuations over all MD steps +should be a multiple of nstcalcenergy. +Note that the exact sums and fluctuations over all MD steps modulo nstcalcenergy are stored in the energy file, so g_energy can report exact energy averages and fluctuations also when nstenergy>1 @@ -391,7 +391,7 @@ energy averages and fluctuations also when nstenergy>1 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 nstlist>0. +energy evaluation when nstlist>0.
0
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 x=0 is not important. More information is in the printed manual.
PME-Switch
-
-A combination of PME and a switch function for the direct-space part -(see above). -rcoulomb is allowed to be smaller than rlist. +
A combination of PME and a switch function for the direct-space part +(see above). rcoulomb is allowed to be smaller than rlist. 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.
PME-User
-
-A combination of PME and user tables (see above). +
A combination of PME and user tables (see above). rcoulomb is allowed to be smaller than rlist. The PME mesh contribution is subtracted from the user table by mdrun. Because of this subtraction the user tables should contain -about 10 decimal places. -
+about 10 decimal places.
PME-User-Switch
-
-A combination of PME-User and a switching function (see above). +
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. -
+i.e. both to the user supplied function and the PME Mesh correction part. @@ -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. +steps of the GROMACS implementation for the current time step pressure.
MTTK
Martyna-Tuckerman-Tobias-Klein implementation, only useable with md-vv @@ -897,7 +891,7 @@ This can be useful for membrane simulations. 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 -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-1].ref_p: [bar]
reference pressure for coupling
refcoord_scaling:
+
no
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.
The reference coordinates are scaled with the scaling matrix of the pressure coupling.
com
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. +
@@ -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.
wall_type:
-
+
9-3
LJ integrated over the volume behind the wall: 9-3 potential
10-4
@@ -1140,7 +1136,7 @@ the energygrp_table option, where the first name is for a ``normal'' energy group and the second name is wall0 or wall1, only the dispersion and repulsion columns are used
-
+
wall_r_linpot: -1 (nm)
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.

COM pulling

pull:
-
+
no
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.
a constant force. For this option there is no reference position and therefore the parameters pull_init and pull_rate are not used.
-
-
pull_geometry
-
+
+
pull_geometry:
+
distance
Pull along the vector connecting the two groups. Components can be selected with pull_dim.
@@ -1213,18 +1209,18 @@ from the COM of the pull group has both a radial and an axial component.
position
Pull to the position of the reference group plus pull_init + time*pull_rate*pull_vec.
-
+
pull_dim: (Y Y Y)
the distance components to be used with geometry distance -and position
, also sets which components are printed -int the output files +and position, and also sets which components are printed +to the output files
pull_r1: (1) [nm]
the inner radius of the cylinder for geometry cylinder
pull_r0: (1) [nm]
the outer radius of the cylinder for geometry cylinder
pull_constr_tol: (1e-6)
the relative constraint tolerance for constraint pulling
-
pull_start
+
pull_start:
no
do not modify pull_init @@ -1435,14 +1431,14 @@ the molecule definition in the topology.
nstdhdl: (10)
the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg, 0 means no ouput, should be a multiple of nstcalcenergy
-
separate_dhdl_file (yes)
+
separate_dhdl_file: (yes)
yes
the free energy values that are calculated (as specified with the foreign-lambda and dhdl_derivatives settings) are written out to a separate file, with the default name dhdl.xvg. This file can be used directly with g_bar.
no
The free energy values are written out to the energy output file (ener.edr, in accumulated blocks at every nstenergy steps), where they can be extracted with g_energy or used directly with g_bar.
-
dh_hist_size (0)
+
dh_hist_size: (0)
If nonzero, specifies the size of the histogram into which the Delta H values (specified with foreign_lambda) 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 foreign lambda and two for the dH/dl, at every nstenergy 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.
dh_hist_spacing (0.1)
Specifies the bin width of the histograms, in energy units. Used in conjunction with dh_hist_size. This size limits the accuracy with which free energies can be calculated. Do not use histograms unless you're certain you need it.
@@ -1523,7 +1519,7 @@ since a cosine of frequency zero has no phase.

Mixed quantum/classical molecular dynamics

-
QMMM: +
QMMM:
no
No QM/MM.
@@ -1537,10 +1533,10 @@ groups at different levels of theory is only possible with the ONIOM QM/MM scheme, specified by QMMMscheme.
-
QMMM-grps: +
QMMM-grps:
groups to be descibed at the QM level
-
QMMMscheme: +
QMMMscheme:
normal
normal QM/MM. There can only be one QMMM-grps that is modelled @@ -1555,37 +1551,37 @@ method by Morokuma and co-workers. There can be more than one QMMM-grps e (QMmethod and QMbasis).
-
QMmethod: (RHF) +
QMmethod: (RHF)
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 CASelectrons and CASorbitals.
-
QMbasis: (STO-3G) +
QMbasis: (STO-3G)
Basisset used to expand the electronic wavefuntion. Only gaussian bassisets 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] +
QMcharge: (0) [integer]
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.
-
QMmult: (1) [integer] +
QMmult: (1) [integer]
The multiplicity of the QMMM-grps. In case there are more than one QMMM-grps, the multiplicity of each ONIOM layer needs to be specified separately.
-
CASorbitals: (0) [integer] +
CASorbitals: (0) [integer]
The number of orbitals to be included in the active space when doing a CASSCF computation.
-
CASelectrons: (0) [integer] +
CASelectrons: (0) [integer]
The number of electrons to be included in the active space when doing a CASSCF computation.
-
SH: +
SH:
no
No surface hopping. The system is always in the electronic @@ -1604,7 +1600,7 @@ method.

Implicit solvent

-
implicit_solvent: +
implicit_solvent:
no
No implicit solvent
@@ -1615,7 +1611,7 @@ OBC. These are specified with the gb_algorithm field. The non-polar solva is specified with the sa_algorithm field.
-
gb_algorithm: +
gb_algorithm:
Still
Use the Still method to calculate the Born radii
@@ -1625,30 +1621,30 @@ is specified with the sa_algorithm field.
Use the Onufriev-Bashford-Case method to calculate the Born radii
-
nstgbradii: (1) [steps] +
nstgbradii: (1) [steps]
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.
-
rgbradii: (1.0) [nm] +
rgbradii: (1.0) [nm]
Cut-off for the calculation of the Born radii. Currently must be equal to rlist
-
gb_epsilon_solvent: (80) +
gb_epsilon_solvent: (80)
Dielectric constant for the implicit solvent
-
gb_saltconc: (0) [M] +
gb_saltconc: (0) [M]
Salt concentration for implicit solvent models, currently not used
-
gb_obc_alpha (1); gb_obc_beta (0.8); gb_obc_gamma (4.85); +
gb_obc_alpha (1); gb_obc_beta (0.8); gb_obc_gamma (4.85);
Scale factors for the OBC model. Default values are OBC(II). Values for OBC(I) are 0.8, 0 and 2.91 respectively
-
gb_dielectric_offset: (0.009) [nm] +
gb_dielectric_offset: (0.009) [nm]
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
-
sa_algorithm +
sa_algorithm
Ace-approximation
Use an Ace-type approximation (default)
@@ -1657,13 +1653,14 @@ for the corresponding atom
calculated -
sa_surface_tension: [kj/mol/nm2] -
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 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 +
sa_surface_tension: [kJ mol-1 nm-2]
+
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/Angstrom2 for Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) -
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.