<li><A HREF="#general"><b>General remarks</b></A>
<p> </p>
<li><A HREF="#pp"><b>preprocessing</b></A> (include, define)
-<li><A HREF="#run"><b>run control</b></A> (integrator, tinit, dt, nsteps, init_step, comm_mode, nstcomm, comm_grps)
-<li><A HREF="#ld"><b>langevin dynamics</b></A> (bd_fric, ld_seed)
+<li><A HREF="#run"><b>run control</b></A> (integrator, tinit, dt, nsteps, init-step, comm-mode, nstcomm, comm-grps)
+<li><A HREF="#ld"><b>langevin dynamics</b></A> (bd-fric, ld-seed)
<li><A HREF="#em"><b>energy minimization</b></A> (emtol, emstep, nstcgsteep)
<li><a HREF="#xmdrun"><b>shell molecular dynamics</b></a>(emtol,niter,fcstep)
<li><a HREF="#tpi"><b>test particle insertion</b></a>(rtpi)
-<li><A HREF="#out"><b>output control</b></A> (nstxout, nstvout, nstfout, nstlog, nstcalcenergy, nstenergy, nstxtcout, xtc_precision, xtc_grps, energygrps)
-<li><A HREF="#nl"><b>neighbor searching</b></A> (nstlist, ns_type, pbc, periodic_molecules, rlist, rlistlong)
-<li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, rcoulomb_switch, rcoulomb, epsilon_r, epsilon_rf)
-<li><A HREF="#vdw"><b>VdW</b></A> (vdwtype, rvdw_switch, rvdw, DispCorr)
-<li><A HREF="#table"><b>tables</b></A> (table-extension, energygrp_table)
-<li><A HREF="#ewald"><b>Ewald</b></A> (fourierspacing, fourier_nx, fourier_ny, fourier_nz, pme_order, ewald_rtol, ewald_geometry, epsilon_surface, optimize_fft)
-<li><A HREF="#tc"><b>Temperature coupling</b></A> (tcoupl, nsttcouple, tc_grps, tau_t, ref_t)
+<li><A HREF="#out"><b>output control</b></A> (nstxout, nstvout, nstfout, nstlog, nstcalcenergy, nstenergy, nstxtcout, xtc-precision, xtc-grps, energygrps)
+<li><A HREF="#nl"><b>neighbor searching</b></A> (nstlist, ns-type, pbc, periodic-molecules, rlist, rlistlong)
+<li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
+<li><A HREF="#vdw"><b>VdW</b></A> (vdwtype, rvdw-switch, rvdw, DispCorr)
+<li><A HREF="#table"><b>tables</b></A> (table-extension, energygrp-table)
+<li><A HREF="#ewald"><b>Ewald</b></A> (fourierspacing, fourier-nx, fourier-ny, fourier-nz, pme-order, ewald-rtol, ewald-geometry, epsilon-surface, optimize-fft)
+<li><A HREF="#tc"><b>Temperature coupling</b></A> (tcoupl, nsttcouple, tc-grps, tau-t, ref-t)
<li><A HREF="#pc"><b>Pressure coupling</b></A> (pcoupl, pcoupltype,
- nstpcouple, tau_p, compressibility, ref_p, refcoord_scaling)
-<li><A HREF="#sa"><b>simulated annealing</b></A> (annealing, annealing_npoints, annealing_time, annealing_temp)
-<li><A HREF="#vel"><b>velocity generation</b></A> (gen_vel, gen_temp, gen_seed)
-<li><A HREF="#bond"><b>bonds</b></A> (constraints, constraint_algorithm, continuation, shake_tol, lincs_order, lincs_iter, lincs_warnangle, morse)
-<li><A HREF="#egexcl"><b>Energy group exclusions</b></A> (energygrp_excl)
-<li><A HREF="#walls"><b>Walls</b></A> (nwall, wall_type, wall_r_linpot, wall_atomtype,
-wall_density, wall_ewald_zfac)
+ nstpcouple, tau-p, compressibility, ref-p, refcoord-scaling)
+<li><A HREF="#sa"><b>simulated annealing</b></A> (annealing, annealing-npoints, annealing-time, annealing-temp)
+<li><A HREF="#vel"><b>velocity generation</b></A> (gen-vel, gen-temp, gen-seed)
+<li><A HREF="#bond"><b>bonds</b></A> (constraints, constraint-algorithm, continuation, shake-tol, lincs-order, lincs-iter, lincs-warnangle, morse)
+<li><A HREF="#egexcl"><b>Energy group exclusions</b></A> (energygrp-excl)
+<li><A HREF="#walls"><b>Walls</b></A> (nwall, wall-type, wall-r-linpot, wall-atomtype,
+wall-density, wall-ewald-zfac)
<li><A HREF="#pull"><b>COM pulling</b></A> (pull, ...)
-<li><A HREF="#nmr"><b>NMR refinement</b></A> (disre, disre_weighting, disre_mixed, disre_fc, disre_tau, nstdisreout, orire, orire_fc, orire_tau, orire_fitgrp, nstorireout)
-<li><A HREF="#free"><b>Free Energy calculations</b></A> (free_energy, init_lambda, delta_lambda, sc_alpha, sc_power, sc_sigma, couple-moltype, couple-lambda0, couple-lambda1, couple-intramol)
-<li><A HREF="#neq"><b>Non-equilibrium MD</b></A> (acc_grps, accelerate, freezegrps, freezedim, cos_acceleration, deform)
-<li><A HREF="#ef"><b>Electric fields</b></A> (E_x, E_xt, E_y, E_yt, E_z, E_zt )
+<li><A HREF="#nmr"><b>NMR refinement</b></A> (disre, disre-weighting, disre-mixed, disre-fc, disre-tau, nstdisreout, orire, orire-fc, orire-tau, orire-fitgrp, nstorireout)
+<li><A HREF="#free"><b>Free Energy calculations</b></A> (free-energy, init-lambda, delta-lambda, sc-alpha, sc-power, sc-sigma, couple-moltype, couple-lambda0, couple-lambda1, couple-intramol)
+<li><A HREF="#neq"><b>Non-equilibrium MD</b></A> (acc-grps, accelerate, freezegrps, freezedim, cos-acceleration, deform)
+<li><A HREF="#ef"><b>Electric fields</b></A> (E-x, E-xt, E-y, E-yt, E-z, E-zt )
<li><A HREF="#qmmm"><b>Mixed quantum/classical dynamics</b></A> (QMMM, QMMM-grps, QMMMscheme, QMmethod, QMbasis, QMcharge, Qmmult, CASorbitals, CASelectrons, SH)
-<li><A HREF="#gbsa"><b>Implicit solvent</b></A> (implicit_solvent, gb_algorithm, nstgbradii, rgbradii, gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta, gb_obc_gamma, gb_dielectric_offset, sa_algorithm, sa_surface_tension)
-<li><A HREF="#user"><b>User defined thingies</b></A> (user1_grps, user2_grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
+<li><A HREF="#gbsa"><b>Implicit solvent</b></A> (implicit-solvent, gb-algorithm, nstgbradii, rgbradii, gb-epsilon-solvent, gb-saltconc, gb-obc-alpha, gb-obc-beta, gb-obc-gamma, gb-dielectric-offset, sa-algorithm, sa-surface-tension)
+<li><A HREF="#adress"><b>AdResS settings</b></A> (adress, adress_type, adress_const_wf, adress_ex_width, adress_hy_width, adress_ex_forcecap, adress_interface_correction, adress_site, adress_reference_coords, adress_tf_grp_names, adress_cg_grp_names)
+<li><A HREF="#user"><b>User defined thingies</b></A> (user1-grps, user2-grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
<li><A HREF="#idx"><b>Index</b></A>
</ul>
</P>
Depending on the computational cost of the force calculation,
this can take a significant part of the simulation time.
The temperature for one or more groups of atoms
-(<b><A HREF="#tc">tc_grps</A></b>)
-is set with <b><A HREF="#tc">ref_t</A></b> [K],
+(<b><A HREF="#tc">tc-grps</A></b>)
+is set with <b><A HREF="#tc">ref-t</A></b> [K],
the inverse friction constant for each group is set with
-<b><A HREF="#tc">tau_t</A></b> [ps].
+<b><A HREF="#tc">tau-t</A></b> [ps].
The parameter <b><A HREF="#tc">tcoupl</A></b> is ignored.
-The random generator is initialized with <b><A HREF="#ld">ld_seed</A></b>.
-When used as a thermostat, an appropriate value for <b>tau_t</b> is 2 ps,
+The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.
+When used as a thermostat, an appropriate value for <b>tau-t</b> is 2 ps,
since this results in a friction that is lower than the internal friction
of water, while it is high enough to remove excess heat
(unless <b>cut-off</b> or <b>reaction-field</b> electrostatics is used).
NOTE: temperature deviations decay twice as fast as with
-a Berendsen thermostat with the same <b>tau_t</b>.</dd>
+a Berendsen thermostat with the same <b>tau-t</b>.</dd>
<dt><b>sd1</b></dt>
<dd> An efficient leap-frog stochastic dynamics integrator.
This integrator is equivalent to <b>sd</b>, except that it requires
-only one Gaussian random number and one constraint step.
-This integrator is less accurate.
-For water the relative error in the temperature with this integrator
-is 0.5 <b>delta_t</b>/<b>tau_t</b>, but for other systems it can be higher.
-Use with care and check the temperature.</dd>
+only one Gaussian random number and one constraint step and is therefore
+significantly faster. Without constraints the accuracy is the same as <b>sd</b>.
+With constraints the accuracy is significantly reduced, so then <b>sd</b>
+will often be preferred.</dd>
<dt><b>bd</b></dt>
<dd>An Euler integrator for Brownian or position Langevin dynamics, the
velocity is the force divided by a friction coefficient
-(<b><A HREF="#ld">bd_fric</A></b> [amu ps<sup>-1</sup>])
-plus random thermal noise (<b><A HREF="#tc">ref_t</A></b>).
-When <b><A HREF="#ld">bd_fric</A></b><tt>=0</tt>, the friction coefficient for each
-particle is calculated as mass/<b><A HREF="#tc">tau_t</A></b>, as for the
+(<b><A HREF="#ld">bd-fric</A></b> [amu ps<sup>-1</sup>])
+plus random thermal noise (<b><A HREF="#tc">ref-t</A></b>).
+When <b><A HREF="#ld">bd-fric</A></b><tt>=0</tt>, the friction coefficient for each
+particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>, as for the
integrator <tt>sd</tt>.
-The random generator is initialized with <b><A HREF="#ld">ld_seed</A></b>.</dd>
+The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.</dd>
<dt><b>steep</b></dt>
<dd>A <!--Idx-->steepest descent<!--EIdx--> algorithm for energy
which is only allowed for single-atom molecules).
Since neighborlist construction is expensive, one can perform several
extra insertions with the same list almost for free.
-The random seed is set with <b><A HREF="#ld">ld_seed</A></b>.
+The random seed is set with <b><A HREF="#ld">ld-seed</A></b>.
The temperature for the Boltzmann weighting is set with
-<b><A HREF="#tc">ref_t</A></b>, this should match the temperature
+<b><A HREF="#tc">ref-t</A></b>, this should match the temperature
of the simulation of the original trajectory.
Dispersion correction is implemented correctly for tpi.
All relevant quantities are written to the file specified with
<tt>sd</tt> and <tt>bd</tt>)</dd>
<dt><b>nsteps: (0)</b></dt>
<dd>maximum number of steps to integrate or minimize, -1 is no maximum</dd>
-<dt><b>init_step: (0)</b></dt>
+<dt><b>init-step: (0)</b></dt>
<dd>The starting step.
-The time at an step i in a run is calculated as: t = <tt>tinit</tt> + <tt>dt</tt>*(<tt>init_step</tt> + i).
-The free-energy lambda is calculated as: lambda = <tt>init_lambda</tt> + <tt>delta_lambda</tt>*(<tt>init_step</tt> + i).
+The time at an step i in a run is calculated as: t = <tt>tinit</tt> + <tt>dt</tt>*(<tt>init-step</tt> + i).
+The free-energy lambda is calculated as: lambda = <tt>init-lambda</tt> + <tt>delta-lambda</tt>*(<tt>init-step</tt> + i).
Also non-equilibrium MD parameters can depend on the step number.
Thus for exact restarts or redoing part of a run it might be necessary to
-set <tt>init_step</tt> to the step number of the restart frame.
+set <tt>init-step</tt> to the step number of the restart frame.
<tt>tpbconv</tt> does this automatically.
</dd>
-<dt><b>comm_mode:</b></dt>
+<dt><b>comm-mode:</b></dt>
<dd><dl compact>
<dt><b>Linear</b></dt>
<dd>Remove center of mass translation</dd>
</dl></dd>
<dt><b>nstcomm: (10) [steps]</b></dt>
<dd>frequency for center of mass motion removal</dd>
-<dt><b>comm_grps:</b></dt>
+<dt><b>comm-grps:</b></dt>
<dd>group(s) for center of mass motion removal, default is the whole system</dd>
</dl>
<h3><!--Idx-->Langevin dynamics<!--EIdx--></h3>
<dl>
-<dt><b>bd_fric: (0) [amu ps<sup>-1</sup>]</b></dt>
+<dt><b>bd-fric: (0) [amu ps<sup>-1</sup>]</b></dt>
<dd>Brownian dynamics friction coefficient.
-When <b>bd_fric</b><tt>=0</tt>, the friction coefficient for each
-particle is calculated as mass/<b><A HREF="#tc">tau_t</A></b>.</dd>
-<dt><b>ld_seed: (1993) [integer]</b></dt>
+When <b>bd-fric</b><tt>=0</tt>, the friction coefficient for each
+particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>.</dd>
+<dt><b>ld-seed: (1993) [integer]</b></dt>
<dd>used to initialize random generator for thermal noise
for stochastic and Brownian dynamics.
-When <b>ld_seed</b> is set to -1, the seed is calculated from the process ID.
+When <b>ld-seed</b> is set to -1, the seed is calculated from the process ID.
When running BD or SD on multiple processors, each processor uses a seed equal
-to <b>ld_seed</b> plus the processor number.</dd>
+to <b>ld-seed</b> plus the processor number.</dd>
</dl>
<A NAME="em"><br>
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>.
energy averages and fluctuations also when <b>nstenergy</b><tt>>1</tt></dd>
<dt><b>nstxtcout: (0) [steps]</b></dt>
<dd>frequency to write coordinates to xtc trajectory</dd>
-<dt><b>xtc_precision: (1000) [real]</b></dt>
+<dt><b>xtc-precision: (1000) [real]</b></dt>
<dd>precision to write to xtc trajectory</dd>
-<dt><b>xtc_grps:</b></dt>
+<dt><b>xtc-grps:</b></dt>
<dd>group(s) to write to xtc trajectory, default the whole system is written
(if <b>nstxtcout</b> > 0)</dd>
<dt><b>energygrps:</b></dt>
<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></dd>
-<dt><b>ns_type:</b></dt>
+<dt><b>ns-type:</b></dt>
<dd><dl compact>
<dt><b>grid</b></dt>
<dd>Make a grid in the box and only check atoms in neighboring grid
<dd>Use no periodic boundary conditions, ignore the box.
To simulate without cut-offs, set all cut-offs to 0 and <b>nstlist</b><tt>=0</tt>.
For best performance without cut-offs, use <b>nstlist</b><tt>=0</tt>,
-<b>ns_type</b><tt>=simple</tt>
+<b>ns-type</b><tt>=simple</tt>
and particle decomposition instead of domain decomposition.</dd>
<dt><b>xy</b></dt>
<dd>Use periodic boundary conditions in x and y directions only.
-This works only with <b>ns_type</b><tt>=grid</tt> and can be used
+This works only with <b>ns-type</b><tt>=grid</tt> and can be used
in combination with <b><a href="#walls">walls</a></b>.
Without walls or with only one wall the system size is infinite
in the z direction. Therefore pressure coupling or Ewald summation
These disadvantages do not apply when two walls are used.</dd>
</dl></dd>
-<dt><b>periodic_molecules:</b></dt>
+<dt><b>periodic-molecules:</b></dt>
<dd><dl compact>
<dt><b>no</b></dt>
<dd>molecules are finite, fast molecular PBC can be used</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>.
Use e.g. <b>rlist</b><tt>=0.9</tt>, <b>rcoulomb</b><tt>=0.9</tt>. The highest magnitude of
wave vectors used in reciprocal space is controlled by <b>fourierspacing</b>.
The relative accuracy of direct/reciprocal space
-is controlled by <b>ewald_rtol</b>.
+is controlled by <b>ewald-rtol</b>.
<br>
NOTE: Ewald scales as O(N<sup>3/2</sup>)
and is thus extremely slow for large systems. It is included mainly for
<dd>Fast Particle-Mesh Ewald electrostatics. Direct space is similar
to the Ewald sum, while the reciprocal part is performed with
FFTs. Grid dimensions are controlled with <b>fourierspacing</b> and the
-interpolation order with <b>pme_order</b>. With a grid spacing of 0.1
+interpolation order with <b>pme-order</b>. With a grid spacing of 0.1
nm and cubic interpolation the electrostatic forces have an accuracy
of 2-3*10<sup>-4</sup>. Since the error from the vdw-cutoff is larger than this you
might try 0.15 nm. When running in parallel the interpolation
<dt><b><!--Idx-->Reaction-Field<!--EIdx--></b></dt>
<dd>Reaction field with Coulomb cut-off <b>rcoulomb</b>,
where <b>rcoulomb</b> ≥ <b>rlist</b>.
-The dielectric constant beyond the cut-off is <b>epsilon_rf</b>.
-The dielectric constant can be set to infinity by setting <b>epsilon_rf</b><tt>=0</tt>.</dd>
+The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
+The dielectric constant can be set to infinity by setting <b>epsilon-rf</b><tt>=0</tt>.</dd>
<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
-<b><A HREF="#tc">ref_t</A></b> [K].</dd>
+<b><A HREF="#tc">ref-t</A></b> [K].</dd>
<dt><b>Reaction-Field-zero</b></dt>
<dd>In GROMACS normal reaction-field electrostatics leads to bad
energy conservation. <b>Reaction-Field-zero</b> solves this
by making the potential zero beyond the cut-off. It can only
-be used with an infinite dielectric constant (<b>epsilon_rf=0</b>),
+be used with an infinite dielectric constant (<b>epsilon-rf=0</b>),
because only for that value the force vanishes at the cut-off.
<b>rlist</b> should be 0.1 to 0.3 nm larger than <b>rcoulomb</b>
to accommodate for the size of charge groups and diffusion
<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
</dl></dd>
<A NAME="el2">
-<dt><b>rcoulomb_switch: (0) [nm]</b></dt>
+<dt><b>rcoulomb-switch: (0) [nm]</b></dt>
<dd>where to start switching the Coulomb potential</dd>
<dt><b>rcoulomb: (1) [nm]</b></dt>
<dd>distance for the Coulomb <!--Idx-->cut-off<!--EIdx--></dd>
-<dt><b>epsilon_r: (1)</b></dt>
+<dt><b>epsilon-r: (1)</b></dt>
<dd>The relative <!--Idx-->dielectric constant<!--EIdx-->.
A value of 0 means infinity.</dd>
-<dt><b>epsilon_rf: (1)</b></dt>
+<dt><b>epsilon-rf: (0)</b></dt>
<dd>The relative dielectric constant of the reaction field.
This is only used with reaction-field electrostatics.
A value of 0 means infinity.</dd>
<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
<dt><b>Switch</b></dt>
<dd>The LJ (not Buckingham)
-potential is normal out to <b>rvdw_switch</b>, after which it is switched
+potential is normal out to <b>rvdw-switch</b>, after which it is switched
off to reach zero at <b>rvdw</b>. Both the potential and force functions
are continuously smooth, but be aware that all switch functions will give rise
to a bulge (increase) in the force (since we are switching the potential).
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>
which are always tabulated irrespective of the use of
tables for the non-bonded interactions. </dd>
-<dt><b>energygrp_table:</b></dt>
+<dt><b>energygrp-table:</b></dt>
<dd>When user tables are used for electrostatics and/or VdW,
here one can give pairs of energy groups for which seperate
user tables should be used.
The two energy groups will be appended to the table file name,
in order of their definition in <b>energygrps</b>, seperated by underscores.
For example, if <tt>energygrps = Na Cl Sol</tt>
-and <tt>energygrp_table = Na Na Na Cl</tt>, <tt>mdrun</tt> will read
+and <tt>energygrp-table = Na Na Na Cl</tt>, <tt>mdrun</tt> will read
<tt>table_Na_Na.xvg</tt> and <tt>table_Na_Cl.xvg</tt> in addition
to the normal <tt>table.xvg</tt> which will be used for all other
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
- <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
when the Coulomb cut-off and the PME grid spacing are scaled
by the same factor.</dd>
-<dt><b>fourier_nx (0) ; fourier_ny (0) ; fourier_nz: (0)</b></dt>
+<dt><b>fourier-nx (0) ; fourier-ny (0) ; fourier-nz: (0)</b></dt>
<dd>Highest magnitude of wave vectors in reciprocal space when using Ewald.</dd>
<dd>Grid size when using PPPM or PME. These values override
<b>fourierspacing</b> per direction. The best choice is powers of
2, 3, 5 and 7. Avoid large primes.</dd>
-<dt><b>pme_order (4)</b></dt>
+<dt><b>pme-order (4)</b></dt>
<dd>Interpolation order for PME. 4 equals cubic interpolation. You might try
6/8/10 when running in parallel and simultaneously decrease grid dimension.</dd>
-<dt><b>ewald_rtol (1e-5)</b></dt>
+<dt><b>ewald-rtol (1e-5)</b></dt>
<dd>The relative strength of the Ewald-shifted direct potential at
-<b>rcoulomb</b> is given by <b>ewald_rtol</b>.
+<b>rcoulomb</b> is given by <b>ewald-rtol</b>.
Decreasing this will give a more accurate direct sum,
but then you need more wave vectors for the reciprocal sum.</dd>
-<dt><b>ewald_geometry: (3d)</b></dt>
+<dt><b>ewald-geometry: (3d)</b></dt>
<dd><dl compact>
<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>
+<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.
This value does not affect the slab 3DC variant of the long range corrections.</dd>
-<dt><b>optimize_fft:</b></dt>
+<dt><b>optimize-fft:</b></dt>
<dd><dl compact>
<dt><b>no</b></dt>
<dd>Don't calculate the optimal FFT plan for the grid at startup.</dd>
<dd>No temperature coupling.</dd>
<dt><b>berendsen</b></dt>
<dd>Temperature coupling with a Berendsen-thermostat to a bath with
-temperature <b>ref_t</b> [K], with time constant <b>tau_t</b> [ps].
+temperature <b>ref-t</b> [K], with time constant <b>tau-t</b> [ps].
Several groups can be coupled separately, these are specified in the
-<b>tc_grps</b> field separated by spaces.</dd>
+<b>tc-grps</b> field separated by spaces.</dd>
<dt><b>nose-hoover</b></dt>
<dd>Temperature coupling using a Nose-Hoover extended
ensemble. The reference temperature and coupling groups are selected
-as above, but in this case <b>tau_t</b> [ps] controls the period
+as above, but in this case <b>tau-t</b> [ps] controls the period
of the temperature fluctuations at equilibrium, which is slightly
different from a relaxation time.
For NVT simulations the conserved energy quantity is written
<dd>Temperature coupling using velocity rescaling with a stochastic term
(JCP 126, 014101).
This thermostat is similar to Berendsen coupling, with the same scaling
-using <b>tau_t</b>, but the stochastic term ensures that a proper
+using <b>tau-t</b>, but the stochastic term ensures that a proper
canonical ensemble is generated. The random seed is set with
-<b><A HREF="#ld">ld_seed</A></b>.
-This thermostat works correctly even for <b>tau_t</b><tt>=0</tt>.
+<b><A HREF="#ld">ld-seed</A></b>.
+This thermostat works correctly even for <b>tau-t</b><tt>=0</tt>.
For NVT simulations the conserved energy quantity is written
to the energy and log file.</dd>
</dl>
</dd>
<dt><b>nh-chain-length (10)</b></dt>
<dd>the number of chained Nose-Hoover thermostats for velocity Verlet integrators, the leap-frog <b>md</b> integrator only supports 1. Data for the NH chain variables is not printed to the .edr, but can be using the <tt>GMX_NOSEHOOVER_CHAINS</tt> environment variable</dd>
-<dt><b>tc_grps:</b></dt>
+<dt><b>tc-grps:</b></dt>
<dd>groups to couple separately to temperature bath</dd>
-<dt><b>tau_t: [ps]</b></dt>
-<dd>time constant for coupling (one for each group in <b>tc_grps</b>),
+<dt><b>tau-t: [ps]</b></dt>
+<dd>time constant for coupling (one for each group in <b>tc-grps</b>),
-1 means no temperature coupling</dd>
-<dt><b>ref_t: [K]</b></dt>
-<dd>reference temperature for coupling (one for each group in <b>tc_grps</b>)</dd>
+<dt><b>ref-t: [K]</b></dt>
+<dd>reference temperature for coupling (one for each group in <b>tc-grps</b>)</dd>
</dl>
<A NAME="pc"><br>
<dd>No pressure coupling. This means a fixed box size.</dd>
<dt><b>berendsen</b></dt>
<dd>Exponential relaxation pressure coupling with time constant
-<b>tau_p</b> [ps]. The box is scaled every timestep. It has been
+<b>tau-p</b> [ps]. The box is scaled every timestep. It has been
argued that this does not yield a correct thermodynamic ensemble,
but it is the most efficient way to scale a box at the beginning
of a run.</dd>
<dd>Extended-ensemble pressure coupling where the box vectors are
subject to an equation of motion. The equation of motion for the atoms
is coupled to this. No instantaneous scaling takes place. As for
-Nose-Hoover temperature coupling the time constant <b>tau_p</b> [ps]
+Nose-Hoover temperature coupling the time constant <b>tau-p</b> [ps]
is the period of pressure fluctuations at equilibrium. This is
probably a better method when you want to apply pressure scaling
during data collection, but beware that you can get very large
<dt><b>MTTK</b></dt>
<dd>Martyna-Tuckerman-Tobias-Klein implementation, only useable with <b>md-vv</b>
or <b>md-vv-avek</b>, very similar to Parrinello-Rahman.
-As for Nose-Hoover temperature coupling the time constant <b>tau_p</b>
+As for Nose-Hoover temperature coupling the time constant <b>tau-p</b>
[ps] is the period of pressure fluctuations at equilibrium. This is
probably a better method when you want to apply pressure scaling
during data collection, but beware that you can get very large
<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>
For velocity Verlet integrators <b>nstpcouple</b> is set to 1.</dd>
</dd>
-<dt><b>tau_p: (1) [ps]</b></dt>
+<dt><b>tau-p: (1) [ps]</b></dt>
<dd>time constant for coupling</dd>
<dt><b>compressibility: [bar<sup>-1</sup>]</b></dt>
<dd>compressibility (NOTE: this is now really in bar<sup>-1</sup>)
For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar<sup>-1</sup>].</dd>
-<dt><b>ref_p: [bar]</b></dt>
+<dt><b>ref-p: [bar]</b></dt>
<dd>reference pressure for coupling</dd>
-<dt><b>refcoord_scaling:</b></dt>
+<dt><b>refcoord-scaling:</b></dt>
<dd><dl compact>
<dt><b>no</b></dt>
<dd>The reference coordinates for position restraints are not modified.
</dd>
</dl>
-<dt><b>annealing_npoints:</b></dt>
+<dt><b>annealing-npoints:</b></dt>
<dd>A list with the number of annealing reference/control points used for
each temperature group. Use 0 for groups that are not annealed. The number of entries should equal the number of temperature groups.</dd>
-<dt><b>annealing_time:</b></dt>
-<dd>List of times at the annealing reference/control points for each group. If you are using periodic annealing, the times will be used modulo the last value, i.e. if the values are 0, 5, 10, and 15, the coupling will restart at the 0ps value after 15ps, 30ps, 45ps, etc. The number of entries should equal the sum of the numbers given in <tt>annealing_npoints</tt>.</dd>
+<dt><b>annealing-time:</b></dt>
+<dd>List of times at the annealing reference/control points for each group. If you are using periodic annealing, the times will be used modulo the last value, i.e. if the values are 0, 5, 10, and 15, the coupling will restart at the 0ps value after 15ps, 30ps, 45ps, etc. The number of entries should equal the sum of the numbers given in <tt>annealing-npoints</tt>.</dd>
-<dt><b>annealing_temp:</b></dt>
-<dd>List of temperatures at the annealing reference/control points for each group. The number of entries should equal the sum of the numbers given in <tt>annealing_npoints</tt>.</dd>
+<dt><b>annealing-temp:</b></dt>
+<dd>List of temperatures at the annealing reference/control points for each group. The number of entries should equal the sum of the numbers given in <tt>annealing-npoints</tt>.</dd>
<br>
-Confused? OK, let's use an example. Assume you have two temperature groups, set the group selections to <tt>annealing = single periodic</tt>, the number of points of each group to <tt>annealing_npoints = 3 4</tt>, the times to <tt>annealing_time = 0 3 6 0 2 4 6</tt> and finally temperatures to <tt>annealing_temp = 298 280 270 298 320 320 298</tt>.
+Confused? OK, let's use an example. Assume you have two temperature groups, set the group selections to <tt>annealing = single periodic</tt>, the number of points of each group to <tt>annealing-npoints = 3 4</tt>, the times to <tt>annealing-time = 0 3 6 0 2 4 6</tt> and finally temperatures to <tt>annealing-temp = 298 280 270 298 320 320 298</tt>.
The first group will be coupled to 298K at 0ps, but the reference temperature will drop linearly to reach 280K at 3ps, and then linearly between 280K and 270K from 3ps to 6ps. After this is stays constant, at 270K. The second group is coupled to 298K at 0ps, it increases linearly to 320K at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it decreases to 298K, and then it starts over with the same pattern again, i.e. rising linearly from 298K to 320K between 6ps and 8ps. Check the summary printed by <tt>grompp</tt> if you are unsure!
</dl>
<h3>Velocity generation</h3>
<dl>
-<dt><b>gen_vel:</b></dt>
+<dt><b>gen-vel:</b></dt>
<dd><dl compact>
<dt><b>no</b></dt>
<dd> Do not generate velocities. The velocities are set to zero
when there are no velocities in the input structure file.</dd>
<dt><b>yes</b></dt>
<dd>Generate velocities in <tt>grompp</tt> according to a Maxwell distribution at
-temperature <b>gen_temp</b> [K], with random seed <b>gen_seed</b>.
+temperature <b>gen-temp</b> [K], with random seed <b>gen-seed</b>.
This is only meaningful with integrator <b><A HREF="#run">md</A></b>.</dd>
</dl></dd>
-<dt><b>gen_temp: (300) [K]</b></dt>
+<dt><b>gen-temp: (300) [K]</b></dt>
<dd>temperature for Maxwell distribution</dd>
-<dt><b>gen_seed: (173529) [integer]</b></dt>
+<dt><b>gen-seed: (173529) [integer]</b></dt>
<dd>used to initialize random generator for random velocities,
-when <b>gen_seed</b> is set to -1, the seed is calculated from
+when <b>gen-seed</b> is set to -1, the seed is calculated from
the process ID number.
</dl>
<dd>Convert all bonds and angles to bond-constraints.</dd>
</dl>
-<dt><b>constraint_algorithm:</b></dt>
+<dt><b>constraint-algorithm:</b></dt>
<dd><dl compact>
<dt><b><!--Idx-->LINCS<!--EIdx--></b></dt>
<dd>LINear Constraint Solver.
With domain decomposition the parallel version P-LINCS is used.
The accuracy in set with
-<b>lincs_order</b>, which sets the number of matrices in the expansion
+<b>lincs-order</b>, which sets the number of matrices in the expansion
for the matrix inversion.
After the matrix inversion correction the algorithm does
an iterative correction to compensate for lengthening due to rotation.
The number of such iterations can be controlled with
-<b>lincs_iter</b>. The root mean square relative constraint deviation
+<b>lincs-iter</b>. The root mean square relative constraint deviation
is printed to the log file every <b>nstlog</b> steps.
-If a bond rotates more than <b>lincs_warnangle</b> [degrees] in one step,
+If a bond rotates more than <b>lincs-warnangle</b> [degrees] in one step,
a warning will be printed both to the log file and to <TT>stderr</TT>.
LINCS should not be used with coupled angle constraints.
</dd>
<dt><b><!--Idx-->SHAKE<!--EIdx--></b></dt>
<dd>SHAKE is slightly slower and less stable than LINCS, but does work with
angle constraints.
-The relative tolerance is set with <b>shake_tol</b>, 0.0001 is a good value
+The relative tolerance is set with <b>shake-tol</b>, 0.0001 is a good value
for ``normal'' MD. SHAKE does not support constraints between atoms
on different nodes, thus it can not be used with domain decompositon
when inter charge-group constraints are present.
</dd>
</dl></dd>
<dt><b>continuation:</b></dt>
-<dd>This option was formerly known as <tt>unconstrained_start</tt>.</dd>
+<dd>This option was formerly known as <tt>unconstrained-start</tt>.</dd>
<dd><dl compact>
<dt><b>no</b></dt>
<dd>apply constraints to the start configuration and reset shells</dd>
</dl></dd>
<A NAME="bond2">
-<dt><b>shake_tol: (0.0001)</b></dt>
+<dt><b>shake-tol: (0.0001)</b></dt>
<dd>relative tolerance for SHAKE</dd>
-<dt><b>lincs_order: (4)</b></dt>
+<dt><b>lincs-order: (4)</b></dt>
<dd>Highest order in the expansion of the constraint coupling matrix.
When constraints form triangles, an additional expansion of the same
order is applied on top of the normal expansion only for the couplings
needed for large time-steps with virtual sites or BD.
For accurate energy minimization an order of 8 or more might be required.
With domain decomposition, the cell size is limited by the distance
-spanned by <b>lincs_order</b>+1 constraints. When one wants to scale
-further than this limit, one can decrease <b>lincs_order</b> and increase
-<b>lincs_iter</b>, since the accuracy does not deteriorate
-when (1+<b>lincs_iter</b>)*<b>lincs_order</b> remains constant.</dd>
-<dt><b>lincs_iter: (1)</b></dt>
+spanned by <b>lincs-order</b>+1 constraints. When one wants to scale
+further than this limit, one can decrease <b>lincs-order</b> and increase
+<b>lincs-iter</b>, since the accuracy does not deteriorate
+when (1+<b>lincs-iter</b>)*<b>lincs-order</b> remains constant.</dd>
+<dt><b>lincs-iter: (1)</b></dt>
<dd>Number of iterations to correct for rotational lengthening in LINCS.
For normal runs a single step is sufficient, but for NVE
runs where you want to conserve energy accurately or for accurate
energy minimization you might want to increase it to 2.
-<dt><b>lincs_warnangle: </b>(30) [degrees]</dt>
+<dt><b>lincs-warnangle: </b>(30) [degrees]</dt>
<dd>maximum angle that a bond can rotate before LINCS will complain</dd>
<dt><b>morse:</b></dt>
<hr>
<h3>Energy group <!--Idx-->exclusions<!--EIdx--></h3>
<dl>
-<dt><b>energygrp_excl: </b></dt>
+<dt><b>energygrp-excl: </b></dt>
<dd>Pairs of energy groups for which all non-bonded interactions are
excluded. An example: if you have two energy groups <tt>Protein</tt>
and <tt>SOL</tt>, specifying
<br>
-<tt>energygrp_excl = Protein Protein SOL SOL</tt>
+<tt>energygrp-excl = Protein Protein SOL SOL</tt>
<br>
would give only the non-bonded interactions between the protein and the
solvent. This is especially useful for speeding up energy calculations with
<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
of each atomtype with the walls.</dd>
-<dt><b>wall_type:</b></dt>
+<dt><b>wall-type:</b></dt>
<dd><dl compact>
<dt><b>9-3</b></dt>
<dd>LJ integrated over the volume behind the wall: 9-3 potential</dd>
<dt><b>12-6</b></dt>
<dd>direct LJ potential with the z distance from the wall</dd>
<dt><b>table</b></dt><dd>user defined potentials indexed with the z distance from the wall, the tables are read analogously to
-the <b><A HREF="#table">energygrp_table</A></b> option,
+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></dd>
-<dt><b>wall_r_linpot: -1 (nm)</b></dt>
+<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
a postive value is especially useful for equilibration when some atoms
are beyond a wall.
-When the value is ≤0 (<0 for <b>wall_type=table</b>),
+When the value is ≤0 (<0 for <b>wall-type=table</b>),
a fatal error is generated when atoms are beyond a wall.
</dd>
-<dt><b>wall_density: [nm<sup>-3</sup>/nm<sup>-2</sup>]</b></dt>
+<dt><b>wall-density: [nm<sup>-3</sup>/nm<sup>-2</sup>]</b></dt>
<dd>the number density of the atoms for each wall for wall types
<b>9-3</b> and <b>10-4</b>
-<dt><b>wall_ewald_zfac: 3</b></dt>
+<dt><b>wall-ewald-zfac: 3</b></dt>
<dd>The scaling factor for the third box vector for Ewald summation only,
the minimum is 2.
Ewald summation can only be used with <b>nwall=2</b>, where one
-should use <b><A HREF="#ewald">ewald_geometry</A><tt>=3dc</tt></b>.
+should use <b><A HREF="#ewald">ewald-geometry</A><tt>=3dc</tt></b>.
The empty layer in the box serves to decrease the unphysical Coulomb
interaction between periodic images.
</dl>
between the reference group and one or more groups.
The setup is identical to the option <b>umbrella</b>, except for the fact
that a rigid constraint is applied instead of a harmonic potential.</dd>
-<dt><b>constant_force</b></dt>
+<dt><b>constant-force</b></dt>
<dd>Center of mass pulling using a linear potential and therefore
a constant force. For this option there is no reference position
-and therefore the parameters <b>pull_init</b> and <b>pull_rate</b>
+and therefore the parameters <b>pull-init</b> and <b>pull-rate</b>
are not used.</dd>
</dl></dd>
-<dt><b>pull_geometry:</b></dt>
+<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>
+Components can be selected with <b>pull-dim</b>.</dd>
<dt><b>direction</b></dt>
-<dd>Pull in the direction of <b>pull_vec</b>.</dd>
-<dt><b>direction_periodic</b></dt>
+<dd>Pull in the direction of <b>pull-vec</b>.</dd>
+<dt><b>direction-periodic</b></dt>
<dd>As <b>direction</b>, but allows the distance to be larger than
half the box size. With this geometry the box should not be dynamic
(e.g. no pressure scaling) in the pull dimensions and the pull force
<dt><b>cylinder</b></dt>
<dd>Designed for pulling with respect to a layer where the reference COM
is given by a local cylindrical part of the reference group.
-The pulling is in the direction of <b>pull_vec</b>.
+The pulling is in the direction of <b>pull-vec</b>.
From the reference group a cylinder is selected around the axis going
-through the pull group with direction <b>pull_vec</b> using two radii.
-The radius <b>pull_r1</b> gives the radius within which all
-the relative weights are one, between <b>pull_r1</b> and
-<b>pull_r0</b> the weights are switched to zero. Mass weighting is also used.
+through the pull group with direction <b>pull-vec</b> using two radii.
+The radius <b>pull-r1</b> gives the radius within which all
+the relative weights are one, between <b>pull-r1</b> and
+<b>pull-r0</b> the weights are switched to zero. Mass weighting is also used.
Note that the radii should be smaller than half the box size.
For tilted cylinders they should be even smaller than half the box size
since the distance of an atom in the reference group
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>
+<b>pull-init</b> + time*<b>pull-rate</b>*<b>pull-vec</b>.</dd>
</dl></dd>
-<dt><b>pull_dim: (Y Y Y)</b></dt>
+<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>, and also sets which components are printed
to the output files</dd>
-<dt><b>pull_r1: (1) [nm]</b></dt>
+<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>
+<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>
+<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>
+<dd>do not modify <b>pull-init</b>
<dt><b>yes</b></dt>
-<dd>add the COM distance of the starting conformation to <b>pull_init</b></dd>
+<dd>add the COM distance of the starting conformation to <b>pull-init</b></dd>
</dl>
-<dt><b>pull_nstxout: (10)</b></dt>
+<dt><b>pull-nstxout: (10)</b></dt>
<dd>frequency for writing out the COMs of all the pull group</dd>
-<dt><b>pull_nstfout: (1)</b></dt>
+<dt><b>pull-nstfout: (1)</b></dt>
<dd>frequency for writing out the force of all the pulled group</dd>
-<dt><b>pull_ngroups: (1)</b></dt>
+<dt><b>pull-ngroups: (1)</b></dt>
<dd>The number of pull groups, not including the reference group.
If there is only one group, there is no difference in treatment
of the reference and pulled group (except with the cylinder geometry).
and the first group (ending on 1) are given,
further groups work analogously, but with the number 1 replaced
by the group number.</dd>
-<dt><b>pull_group0: </b></dt>
+<dt><b>pull-group0: </b></dt>
<dd>The name of the reference group. When this is empty an absolute reference
of (0,0,0) is used. With an absolute reference the system is no longer
translation invariant and one should think about what to do with
the <A HREF="#run">center of mass motion</A>.</dd>
-<dt><b>pull_weights0: </b></dt>
-<dd>see <b>pull_weights1</b></dd>
-<dt><b>pull_pbcatom0: (0)</b></dt>
-<dd>see <b>pull_pbcatom1</b></dd>
-<dt><b>pull_group1: </b></dt>
+<dt><b>pull-weights0: </b></dt>
+<dd>see <b>pull-weights1</b></dd>
+<dt><b>pull-pbcatom0: (0)</b></dt>
+<dd>see <b>pull-pbcatom1</b></dd>
+<dt><b>pull-group1: </b></dt>
<dd>The name of the pull group.</dd>
-<dt><b>pull_weights1: </b></dt>
+<dt><b>pull-weights1: </b></dt>
<dd>Optional relative weights which are multiplied with the masses of the atoms
to give the total weight for the COM. The number should be 0, meaning all 1,
or the number of atoms in the pull group.</dd>
-<dt><b>pull_pbcatom1: (0)</b></dt>
+<dt><b>pull-pbcatom1: (0)</b></dt>
<dd>The reference atom for the treatment of periodic boundary conditions
inside the group
(this has no effect on the treatment of the pbc between groups).
This option is only important when the diameter of the pull group
is larger than half the shortest box vector.
For determining the COM, all atoms in the group are put at their periodic image
-which is closest to <b>pull_pbcatom1</b>.
+which is closest to <b>pull-pbcatom1</b>.
A value of 0 means that the middle atom (number wise) is used.
This parameter is not used with geometry <b>cylinder</b>.
A value of -1 turns on cosine weighting, which is useful for a group
of molecules in a periodic system, e.g. a water slab (see Engin et al.
J. Chem. Phys. B 2010).</dd>
-<dt><b>pull_vec1: (0.0 0.0 0.0)</b></dt>
+<dt><b>pull-vec1: (0.0 0.0 0.0)</b></dt>
<dd>The pull direction. <tt>grompp</tt> normalizes the vector.</dd>
-<dt><b>pull_init1: (0.0) / (0.0 0.0 0.0) [nm]</b></dt>
+<dt><b>pull-init1: (0.0) / (0.0 0.0 0.0) [nm]</b></dt>
<dd>The reference distance at t=0. This is a single value,
except for geometry <b>position</b> which uses a vector.</dd>
-<dt><b>pull_rate1: (0) [nm/ps]</b></dt>
+<dt><b>pull-rate1: (0) [nm/ps]</b></dt>
<dd>The rate of change of the reference position.</dd>
-<dt><b>pull_k1: (0) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
+<dt><b>pull-k1: (0) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
<dd>The force constant. For umbrella pulling this is the harmonic force
constant in [kJ mol<sup>-1</sup> nm<sup>-2</sup>]. For constant force pulling
this is the force constant of the linear potential, and thus minus (!)
the constant force in [kJ mol<sup>-1</sup> nm<sup>-1</sup>].</dd>
-<dt><b>pull_kB1: (pull_k1) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
-<dd>As <b>pull_k1</b>, but for state B. This is only used when
-<A HREF="#free"><b>free_energy</b></A> is turned on.
-The force constant is then (1 - lambda)*<b>pull_k1</b> + lambda*<b>pull_kB1</b>.
+<dt><b>pull-kB1: (pull-k1) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
+<dd>As <b>pull-k1</b>, but for state B. This is only used when
+<A HREF="#free"><b>free-energy</b></A> is turned on.
+The force constant is then (1 - lambda)*<b>pull-k1</b> + lambda*<b>pull-kB1</b>.
</dl>
<A NAME="nmr"><br>
should only be used for special cases, such as dimers
(this option is not fuctional in the current version of GROMACS)</dd>
</dl></dd>
-<dt><b>disre_weighting:</b></dt>
+<dt><b>disre-weighting:</b></dt>
<dd><dl compact>
<dt><b>conservative</b></dt>
<dd>the forces are the derivative of the restraint potential,
<dt><b>equal</b></dt>
<dd>divide the restraint force equally over all atom pairs in the restraint</dd>
</dl></dd>
-<dt><b>disre_mixed:</b></dt>
+<dt><b>disre-mixed:</b></dt>
<dd><dl compact>
<dt><b>no</b></dt>
<dd>the violation used in the calculation of the restraint force is the
square root of the time averaged violation times the instantaneous violation </dd>
</dl></dd>
-<dt><b>disre_fc: (1000) [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
+<dt><b>disre-fc: (1000) [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
<dd>force constant for distance restraints, which is multiplied by a
(possibly) different factor for each restraint</dd>
-<dt><b>disre_tau: (0) [ps]</b></dt>
+<dt><b>disre-tau: (0) [ps]</b></dt>
<dd>time constant for distance restraints running average</dd>
<dt><b>nstdisreout: (100) [steps]</b></dt>
<dd>use orientation restraints, ensemble averaging can be performed
with <tt>mdrun -multi</tt></dd>
</dl>
-<dt><b>orire_fc: (0) [kJ mol]</b></dt>
+<dt><b>orire-fc: (0) [kJ mol]</b></dt>
<dd>force constant for orientation restraints, which is multiplied by a
(possibly) different factor for each restraint, can be set to zero to
obtain the orientations from a free simulation</dd>
-<dt><b>orire_tau: (0) [ps]</b></dt>
+<dt><b>orire-tau: (0) [ps]</b></dt>
<dd>time constant for orientation restraints running average</dd>
-<dt><b>orire_fitgrp: </b></dt>
+<dt><b>orire-fitgrp: </b></dt>
<dd>fit group for orientation restraining, for a protein backbone is a good
choice</dd>
<dt><b>nstorireout: (100) [steps]</b></dt>
<h3><!--Idx-->Free energy calculations<!--EIdx--></h3>
<dl>
-<dt><b>free_energy:</b></dt>
+<dt><b>free-energy:</b></dt>
<dd><dl compact>
<dt><b>no</b></dt>
<dd>Only use topology A.</dd>
<dt><b>yes</b></dt>
<dd>Interpolate between topology A (lambda=0) to topology B (lambda=1)
-and write the derivative of the Hamiltonian with respect to lambda (as specified with <b>dhdl_derivatives</b>), or the Hamiltonian differences with respect to other lambda values (as specified with <b>foreign_lambda</b>) to
+and write the derivative of the Hamiltonian with respect to lambda (as specified with <b>dhdl-derivatives</b>), or the Hamiltonian differences with respect to other lambda values (as specified with <b>foreign-lambda</b>) to
the energy file and/or to <tt>dhdl.xvg</tt>, where they can be processed by, for example <tt>g_bar</tt>.
The potentials, bond-lengths and angles are interpolated linearly as
-described in the manual. When <b>sc_alpha</b> is larger than zero, soft-core
+described in the manual. When <b>sc-alpha</b> is larger than zero, soft-core
potentials are used for the LJ and Coulomb interactions.</dd>
</dl></dd>
-<dt><b>init_lambda: (0)</b></dt>
+<dt><b>init-lambda: (0)</b></dt>
<dd>starting value for lambda</dd>
-<dt><b>delta_lambda: (0)</b></dt>
+<dt><b>delta-lambda: (0)</b></dt>
<dd>increment per time step for lambda</dd>
-<dt><b>foreign_lambda: ()</b></dt>
+<dt><b>foreign-lambda: ()</b></dt>
<dd>Zero, one or more lambda values for which Delta H values will
be determined and written to dhdl.xvg every <b>nstdhdl</b> steps.
Free energy differences between different lambda values can then
be determined with <tt>g_bar</tt>.</dd>
-<dt><b>dhdl_derivatives: (yes)</b></dt>
+<dt><b>dhdl-derivatives: (yes)</b></dt>
<dd>If yes (the default), the derivatives of the Hamiltonian with respect to lambda at each <b>nstdhdl</b> step are written out. These values are needed for interpolation of linear energy differences with <tt>g_bar</tt> (although the same can also be achieved with the right <b>foreign lambda</b> setting, that may not be as flexible), or with thermodynamic integration</dd>
-<dt><b>sc_alpha: (0)</b></dt>
+<dt><b>sc-alpha: (0)</b></dt>
<dd>the soft-core parameter, a value of 0 results in linear interpolation of
the LJ and Coulomb interactions</dd>
-<dt><b>sc_power: (0)</b></dt>
+<dt><b>sc-power: (0)</b></dt>
<dd>the power for lambda in the soft-core function,
only the values 1 and 2 are supported</dd>
-<dt><b>sc_sigma: (0.3) [nm]</b></dt>
+<dt><b>sc-sigma: (0.3) [nm]</b></dt>
<dd>the soft-core sigma for particles which have a C6 or C12 parameter equal
-to zero or a sigma smaller than <b>sc_sigma</b></dd>
+to zero or a sigma smaller than <b>sc-sigma</b></dd>
<dt><b>couple-moltype:</b></dt>
<dd>Here one can supply a molecule type (as defined in the topology)
for calculating solvation or coupling free energies.
There is a special option <b>system</b> that couples all molecule types
in the system. This can be useful for equilibrating a system
starting from (nearly) random coordinates.
-<b>free_energy</b> has to be turned on.
+<b>free-energy</b> has to be turned on.
The Van der Waals interactions and/or charges in this molecule type can be
turned on or off between lambda=0 and lambda=1, depending on the settings
of <b>couple-lambda0</b> and <b>couple-lambda1</b>. If you want to decouple
<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>
+<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>
-<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>
+<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>
</dl>
<h3><!--Idx-->Non-equilibrium MD<!--EIdx--></h3>
<dl>
-<dt><b>acc_grps: </b></dt>
+<dt><b>acc-grps: </b></dt>
<dd>groups for constant acceleration (e.g.: <tt>Protein Sol</tt>)
all atoms in groups Protein and Sol will experience constant acceleration
as specified in the <b>accelerate</b> line</dd>
<dt><b>accelerate: (0) [nm ps<sup>-2</sup>]</b></dt>
-<dd>acceleration for <b>acc_grps</b>; x, y and z for each group
+<dd>acceleration for <b>acc-grps</b>; x, y and z for each group
(e.g. <tt>0.1 0.0 0.0 -0.1 0.0 0.0</tt> means that first group has constant
acceleration of 0.1 nm ps<sup>-2</sup> in X direction, second group the
opposite).</dd>
(e.g. <tt>Y Y N N N N</tt> means that particles in the first group
can move only in Z direction. The particles in the second group can
move in any direction).</dd>
-<dt><b>cos_acceleration: (0) [nm ps<sup>-2</sup>]</b></dt>
+<dt><b>cos-acceleration: (0) [nm ps<sup>-2</sup>]</b></dt>
<dd>the amplitude of the acceleration profile for calculating the
<!--Idx-->viscosity<!--EIdx-->.
The acceleration is in the X-direction and the magnitude is
-<b>cos_acceleration</b> cos(2 pi z/boxheight).
+<b>cos-acceleration</b> cos(2 pi z/boxheight).
Two terms are added to the energy file:
the amplitude of the velocity profile and 1/viscosity.</dd>
<dt><b><!--Idx-->deform<!--EIdx-->: (0 0 0 0 0 0) [nm ps<sup>-1</sup>]</b></dt>
<h3><!--Idx-->Electric field<!--EIdx-->s</h3>
<dl>
-<dt><b>E_x ; E_y ; E_z:</b></dt>
+<dt><b>E-x ; E-y ; E-z:</b></dt>
<dd>If you want to use an electric field in a direction, enter 3 numbers
-after the appropriate <b>E_*</b>, the first number: the number of cosines,
+after the appropriate <b>E-*</b>, the first number: the number of cosines,
only 1 is implemented (with frequency 0) so enter 1,
the second number: the strength of the electric field in
<b>V nm<sup>-1</sup></b>,
the third number: the phase of the cosine, you can enter any number here
since a cosine of frequency zero has no phase.</dd>
-<dt><b>E_xt; E_yt; E_zt: </b></dt>
+<dt><b>E-xt; E-yt; E-zt: </b></dt>
<dd>not implemented yet</dd>
</dl>
<br>
<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>
<h3>Implicit solvent</h3>
<dl>
-<dt><b>implicit_solvent:</b></dt>
+<dt><b>implicit-solvent:</b></dt>
<dd><dl compact="compact">
<dt><b>no</b></dt>
<dd>No implicit solvent</dd>
<dt><b>GBSA</b></dt>
<dd>Do a simulation with implicit solvent using the Generalized Born formalism.
Three different methods for calculating the Born radii are available, Still, HCT and
-OBC. These are specified with the <b>gb_algorithm</b> field. The non-polar solvation
-is specified with the <b>sa_algorithm</b> field.</dd>
+OBC. These are specified with the <b>gb-algorithm</b> field. The non-polar solvation
+is specified with the <b>sa-algorithm</b> field.</dd>
</dl>
-<dt><b>gb_algorithm:</b></dt>
+<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>
<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><b>gb_epsilon_solvent: (80)</b></dt>
+<dt><b>gb-epsilon-solvent: (80)</b></dt>
<dd>Dielectric constant for the implicit solvent</dd>
-<dt><b>gb_saltconc: (0) [M]</b></dt>
+<dt><b>gb-saltconc: (0) [M]</b></dt>
<dd>Salt concentration for implicit solvent models, currently not used</dd>
-<dt><b>gb_obc_alpha (1); gb_obc_beta (0.8); gb_obc_gamma (4.85);</b></dt>
+<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><b>gb_dielectric_offset: (0.009) [nm]</b></dt>
+<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><b>sa_algorithm</b></dt>
+<dt><b>sa-algorithm</b></dt>
<dd><dl compact="compact">
<dt><b>Ace-approximation</b></dt>
<dd>Use an Ace-type approximation (default)</dd>
calculated</dd>
</dl>
-<dt><b>sa_surface_tension: [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
+<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 <tt>grompp</tt> 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)
-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>
+<A NAME="adress"><br>
+<hr>
+<h3>Adaptive Resolution Simulation</h3>
+
+<dl>
+<dt><b>adress: (no)</b></dt>
+<dd>Decide whether the AdResS feature is turned on.</dd>
+<dt><b>adress-type: (Off)</b></dt>
+<dd><dl compact>
+<dt><b>Off</b></dt>
+<dd>Do an AdResS simulation with weight equal 1, which is equivalent to an explicit (normal) MD simulation. The difference to disabled AdResS is that the AdResS variables are still read-in and hence are defined.</dd>
+<dt><b>Constant</b></dt>
+<dd>Do an AdResS simulation with a constant weight, <b>adress-const-wf</b> defines the value of the weight</dd>
+<dt><b>XSplit</b></dt>
+<dd>Do an AdResS simulation with simulation box split in x-direction, so basically the weight is only a function of the x coordinate and all distances are measured using the x coordinate only.</dd>
+<dt><b>Sphere</b></dt>
+<dd>Do an AdResS simulation with spherical explicit zone.</dd>
+</dl></dd>
+<dt><b>adress-const-wf: (1)</b></dt>
+<dd>Provides the weight for a constant weight simulation (<b>adress-type</b>=Constant)</dd>
+<dt><b>adress-ex-width: (0)</b></dt>
+<dd>Width of the explicit zone, measured from <b>adress-reference-coords</b>.</dd>
+<dt><b>adress-hy-width: (0)</b></dt>
+<dd>Width of the hybrid zone.</dd>
+<dt><b>adress-reference-coords: (0,0,0)</b></dt>
+<dd>Position of the center of the explicit zone. Periodic boundary conditions apply for measuring the distance from it.</dd>
+<dt><b>adress-cg-grp-names</b></dt>
+<dd>The names of the coarse-grained energy groups. All other energy groups are considered explicit and their interactions will be automatically excluded with the coarse-grained groups.</dd>
+<dt><b>adress-site: (COM)</b>The mapping point from which the weight is calculated.</dt>
+<dd><dl compact>
+<dt><b>COM</b></dt>
+<dd>The weight is calculated from the center of mass of each charge group.</dd>
+<dt><b>COG</b></dt>
+<dd>The weight is calculated from the center of geometry of each charge group.</dd>
+<dt><b>Atom</b></dt>
+<dd>The weight is calculated from the position of 1st atom of each charge group.</dd>
+<dt><b>AtomPerAtom</b></dt>
+<dd>The weight is calculated from the position of each individual atom.</dd>
+</dl></dd>
+<dt><b>adress-interface-correction: (Off)</b></dt>
+<dd><dl compact>
+<dt><b>Off</b></dt>
+<dd>Do not a apply any interface correction.</dd>
+<dt><b>thermoforce</b></dt>
+<dd>Apply thermodynamic force interface correction. The table can be specified using the <tt>-tabletf</tt> option of <tt>mdrun</tt>. The table should contain the potential and force (acting on molecules) as function of the distance from <b>adress-reference-coords</b>.</dd>
+</dl></dd>
+<dt><b>adress-tf-grp-names</b></dt>
+<dd>The names of the energy groups to which the <b>thermoforce</b> is applied if enabled in <b>adress-interface-correction</b>. If no group is given the default table is applied.</dd>
+<dt><b>adress-ex-forcecap: (0)</b></dt>
+<dd>Cap the force in the hybrid region, useful for big molecules. 0 disables force capping.</dd>
+</dl>
+
<A NAME="user"><br>
<hr>
<h3>User defined thingies</h3>
<dl>
-<dt><b>user1_grps; user2_grps: </b></dt>
+<dt><b>user1-grps; user2-grps: </b></dt>
<dt><b>userint1 (0); userint2 (0); userint3 (0); userint4 (0)</b></dt>
<dt><b>userreal1 (0); userreal2 (0); userreal3 (0); userreal4 (0)</b></dt>
<dd>These you can use if you modify code. You can pass integers and
<P>
<multicol cols=4>
-<A HREF="#neq">acc_grps</A><br>
+<A HREF="#neq">acc-grps</A><br>
<A HREF="#neq">accelerate</A><br>
<A HREF="#sa">annealing</A><br>
-<A HREF="#sa">annealing_npoints</A><br>
-<A HREF="#sa">annealing_time</A><br>
-<A HREF="#sa">annealing_temp</A><br>
-<A HREF="#ld">bd_fric</A><br>
+<A HREF="#sa">annealing-npoints</A><br>
+<A HREF="#sa">annealing-time</A><br>
+<A HREF="#sa">annealing-temp</A><br>
+<A HREF="#ld">bd-fric</A><br>
<A HREF="#vdw">bDispCorr</A><br>
-<A HREF="#run">comm_mode</A><br>
-<A HREF="#run">comm_grps</A><br>
+<A HREF="#run">comm-mode</A><br>
+<A HREF="#run">comm-grps</A><br>
<A HREF="#pc">compressibility</A><br>
-<A HREF="#bond">constraint_algorithm</A><br>
+<A HREF="#bond">constraint-algorithm</A><br>
<A HREF="#bond">constraints</A><br>
-<A HREF="#neq">cos_acceleration</A><br>
+<A HREF="#neq">cos-acceleration</A><br>
<A HREF="#el">coulombtype</A><br>
<A HREF="#free">couple-intramol</A><br>
<A HREF="#free">couple-lambda0</A><br>
<A HREF="#free">couple-moltype</A><br>
<A HREF="#pp">define</A><br>
<A HREF="#neq">deform</A><br>
-<A HREF="#free">delta_lambda</A><br>
+<A HREF="#free">delta-lambda</A><br>
<A HREF="#nmr">disre</A><br>
-<A HREF="#nmr">disre_weighting</A><br>
-<A HREF="#nmr">disre_mixed</A><br>
-<A HREF="#nmr">disre_fc</A><br>
-<A HREF="#nmr">disre_tau</A><br>
+<A HREF="#nmr">disre-weighting</A><br>
+<A HREF="#nmr">disre-mixed</A><br>
+<A HREF="#nmr">disre-fc</A><br>
+<A HREF="#nmr">disre-tau</A><br>
<A HREF="#run">dt</A><br>
<A HREF="#em">emstep</A><br>
<A HREF="#em">emtol</A><br>
-<A HREF="#egexcl">energygrp_excl</A><br>
-<A HREF="#table">energygrp_table</A><br>
+<A HREF="#egexcl">energygrp-excl</A><br>
+<A HREF="#table">energygrp-table</A><br>
<A HREF="#out">energygrps</A><br>
-<A HREF="#el2">epsilon_r</A><br>
-<A HREF="#el2">epsilon_rf</A><br>
-<A HREF="#ewald">ewald_rtol</A><br>
-<A HREF="#ewald">ewald_geometry</A><br>
-<A HREF="#ewald">epsilon_surface</A><br>
-<A HREF="#ef">E_x</A><br>
-<A HREF="#ef">E_xt</A><br>
-<A HREF="#ef">E_y</A><br>
-<A HREF="#ef">E_yt</A><br>
-<A HREF="#ef">E_z</A><br>
-<A HREF="#ef">E_zt </A><br>
+<A HREF="#el2">epsilon-r</A><br>
+<A HREF="#el2">epsilon-rf</A><br>
+<A HREF="#ewald">ewald-rtol</A><br>
+<A HREF="#ewald">ewald-geometry</A><br>
+<A HREF="#ewald">epsilon-surface</A><br>
+<A HREF="#ef">E-x</A><br>
+<A HREF="#ef">E-xt</A><br>
+<A HREF="#ef">E-y</A><br>
+<A HREF="#ef">E-yt</A><br>
+<A HREF="#ef">E-z</A><br>
+<A HREF="#ef">E-zt </A><br>
<A HREF="#xmdrun">fcstep</A><br>
-<A HREF="#ewald">fourier_nx</A><br>
-<A HREF="#ewald">fourier_ny</A><br>
-<A HREF="#ewald">fourier_nz</A><br>
+<A HREF="#ewald">fourier-nx</A><br>
+<A HREF="#ewald">fourier-ny</A><br>
+<A HREF="#ewald">fourier-nz</A><br>
<A HREF="#ewald">fourierspacing</A><br>
-<A HREF="#free">free_energy</A><br>
+<A HREF="#free">free-energy</A><br>
<A HREF="#neq">freezedim </A><br>
<A HREF="#neq">freezegrps</A><br>
-<A HREF="#vel">gen_seed</A><br>
-<A HREF="#vel">gen_temp</A><br>
-<A HREF="#vel">gen_vel</A><br>
+<A HREF="#vel">gen-seed</A><br>
+<A HREF="#vel">gen-temp</A><br>
+<A HREF="#vel">gen-vel</A><br>
<A HREF="#pp">include</A><br>
-<A HREF="#free">init_lambda</A><br>
-<A HREF="#run">init_step</A><br>
+<A HREF="#free">init-lambda</A><br>
+<A HREF="#run">init-step</A><br>
<A HREF="#run">integrator</A><br>
-<A HREF="#ld">ld_seed</A><br>
-<A HREF="#bond2">lincs_iter</A><br>
-<A HREF="#bond2">lincs_order</A><br>
-<A HREF="#bond2">lincs_warnangle</A><br>
+<A HREF="#ld">ld-seed</A><br>
+<A HREF="#bond2">lincs-iter</A><br>
+<A HREF="#bond2">lincs-order</A><br>
+<A HREF="#bond2">lincs-warnangle</A><br>
<A HREF="#bond2">morse</A><br>
<A HREF="#em">nbfgscorr</A><br>
<A HREF="#xmdrun">niter</A><br>
<A HREF="#out">nstvout</A><br>
<A HREF="#out">nstxout</A><br>
<A HREF="#out">nstxtcout</A><br>
-<A HREF="#nl">ns_type</A><br>
+<A HREF="#nl">ns-type</A><br>
<A HREF="#wall">nwall</A><br>
-<A HREF="#ewald">optimize_fft</A><br>
+<A HREF="#ewald">optimize-fft</A><br>
<A HREF="#nmr2">orire</A><br>
-<A HREF="#nmr2">orire_fc</A><br>
-<A HREF="#nmr2">orire_tau</A><br>
-<A HREF="#nmr2">orire_fitgrp</A><br>
+<A HREF="#nmr2">orire-fc</A><br>
+<A HREF="#nmr2">orire-tau</A><br>
+<A HREF="#nmr2">orire-fitgrp</A><br>
<A HREF="#nmr2">nstorireout</A><br>
<A HREF="#nl">pbc</A><br>
<A HREF="#pc">pcoupl</A><br>
<A HREF="#pc">pcoupltype</A><br>
-<A HREF="#nl">periodic_molecules</A><br>
-<A HREF="#ewald">pme_order</A><br>
+<A HREF="#nl">periodic-molecules</A><br>
+<A HREF="#ewald">pme-order</A><br>
<A HREF="#pull">pull</A><br>
-<A HREF="#pc">refcoord_scaling</A><br>
-<A HREF="#pc">ref_p</A><br>
-<A HREF="#tc">ref_t</A><br>
-<A HREF="#el2">rcoulomb_switch</A><br>
+<A HREF="#pc">refcoord-scaling</A><br>
+<A HREF="#pc">ref-p</A><br>
+<A HREF="#tc">ref-t</A><br>
+<A HREF="#el2">rcoulomb-switch</A><br>
<A HREF="#el2">rcoulomb</A><br>
<A HREF="#nl">rlist</A><br>
<A HREF="#nl">rlistlong</A><br>
<A HREF="#tpi">rtpi</A><br>
-<A HREF="#vdw">rvdw_switch</A><br>
+<A HREF="#vdw">rvdw-switch</A><br>
<A HREF="#vdw">rvdw</A><br>
-<A HREF="#free">sc_alpha</A><br>
-<A HREF="#free">sc_power</A><br>
-<A HREF="#free">sc_sigma</A><br>
-<A HREF="#bond2">shake_tol</A><br>
+<A HREF="#free">sc-alpha</A><br>
+<A HREF="#free">sc-power</A><br>
+<A HREF="#free">sc-sigma</A><br>
+<A HREF="#bond2">shake-tol</A><br>
<A HREF="#table">table-extension</A><br>
-<A HREF="#pc">tau_p</A><br>
-<A HREF="#tc">tau_t</A><br>
-<A HREF="#tc">tc_grps</A><br>
+<A HREF="#pc">tau-p</A><br>
+<A HREF="#tc">tau-t</A><br>
+<A HREF="#tc">tc-grps</A><br>
<A HREF="#tc">tcoupl</A><br>
<A HREF="#run">tinit</A><br>
<A HREF="#bond">continuation</A><br>
-<A HREF="#user">user1_grps</A><br>
-<A HREF="#user">user2_grps</A><br>
+<A HREF="#user">user1-grps</A><br>
+<A HREF="#user">user2-grps</A><br>
<A HREF="#user">userint1</A><br>
<A HREF="#user">userint2</A><br>
<A HREF="#user">userint3</A><br>
<A HREF="#user">userreal3</A><br>
<A HREF="#user">userreal4</A><br>
<A HREF="#el">vdwtype</A><br>
-<A HREF="#out">xtc_grps</A><br>
-<A HREF="#out">xtc_precision</A><br>
-<A HREF="#sa">zero_temp_time</A><br>
-<A HREF="#walls">wall_atomtype</A><br>
-<A HREF="#walls">wall_density</A><br>
-<A HREF="#walls">wall_ewald_zfac</A><br>
-<A HREF="#walls">wall_r_linpot</A><br>
-<A HREF="#walls">wall_type</A><br>
+<A HREF="#out">xtc-grps</A><br>
+<A HREF="#out">xtc-precision</A><br>
+<A HREF="#sa">zero-temp-time</A><br>
+<A HREF="#walls">wall-atomtype</A><br>
+<A HREF="#walls">wall-density</A><br>
+<A HREF="#walls">wall-ewald-zfac</A><br>
+<A HREF="#walls">wall-r-linpot</A><br>
+<A HREF="#walls">wall-type</A><br>
</multicol>
<hr>
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff