256, but each atom can only belong to six different groups, one
each of the following:
\begin{description}
-\item[temperature-coupling group \swapindex{temperature-coupling}{group}]
+\item[\swapindex{temperature-coupling}{group}]
The \normindex{temperature coupling} parameters (reference
temperature, time constant, number of degrees of freedom, see
\ssecref{update}) can be defined for each T-coupling group
$\ve{F}_i = \sum_j \ve{F}_{ij}$ \\
plus the forces due to bonded interactions (which may depend on 1, 2,
3, or 4 atoms), plus restraining and/or external forces. \\
-The potential and kinetic energies and the pressure tensor are computed. \\
+The potential and kinetic energies and the pressure tensor may be computed. \\
$\Downarrow$\\
{\bf 3. Update configuration} \\[1ex]
The movement of the atoms is simulated by numerically solving Newton's
performance and feature support. The group scheme can be made to work
(almost) like the Verlet scheme, but this will lead to a decrease in
performance. The group scheme is especially fast for water molecules,
-which are abundant in many simulations.
+which are abundant in many simulations, but on the most recent x86
+processors, this advantage is negated by the better instruction-level
+parallelism available in the Verlet-scheme implementation. The group
+scheme is deprecated in version 5.0, and will be removed in a future
+version.
In the group scheme, a neighbor list is generated consisting of pairs
of groups of at least one atom. These groups were originally
also uses clusters of atoms, but these are not static as in the group
scheme. Rather, the clusters are defined spatially and consist of 4 or
8 atoms, which is convenient for stream computing, using e.g. SSE, AVX
-or CUDA on GPUs. At neighbor search steps, an atom pair list (or
-cluster pair list, but that's an implementation detail) is created
-with a Verlet buffer. Thus the pair-list cut-off is larger than the
+or CUDA on GPUs. At neighbor search steps, a pair list is created
+with a Verlet buffer, ie. the pair-list cut-off is larger than the
interaction cut-off. In the non-bonded force kernels, forces are only
added when an atom pair is within the cut-off distance at that
particular time step. This ensures that as atoms move between pair
search steps, forces between nearly all atoms within the cut-off
distance are calculated. We say {\em nearly} all atoms, because
{\gromacs} uses a fixed pair list update frequency for
-efficiency. There is a small chance that an atom pair distance is
-decreased to within the cut-off in this fixed number of steps. This
-small chance results in a small energy drift. When temperature
+efficiency. An atom-pair, whose distance was outside the cut-off,
+could possibly move enough during this fixed number of
+steps that its distance is now within the cut-off. This
+small chance results in a small energy drift, and the size of the
+chance depends on the temperature. When temperature
coupling is used, the buffer size can be determined automatically,
-given a certain limit on the energy drift.
+given a certain tolerance on the energy drift.
-The Verlet scheme specific settings in the {\tt mdp} file are:
+The {\tt mdp} file settings specific to the Verlet scheme are:
\begin{verbatim}
cutoff-scheme = Verlet
verlet-buffer-tolerance = 0.005
errors in pair energies cancel and the effect on the total energy drift
is usually at least an order of magnitude smaller than the tolerance.
Furthermore, the drift of the total energy is affected by many other
-factors, the constraint contribution is often the dominating one.
-For constant energy (NVE) simulations, this drift should be set to -1
-and a buffer has to be set manually by specifying {\tt rlist} $>$ {\tt
- rcoulomb}. The simplest way to get a reasonable buffer size is to
-use an NVT {\tt mdp} file with the target temperature set to what you
+factors; often, the contribution from the constraint algorithm dominates.
+
+For constant-energy (NVE) simulations, the buffer size will be
+inferred from the temperature that corresponds to the velocities
+(either those generated, if applicable, or those found in the input
+configuration). Alternatively, the tolerance can be set to -1 and a
+buffer set manually by specifying {\tt rlist} $>$ {\tt max(rcoulomb,
+ rvdw)}. The simplest way to get a reasonable buffer size is to use
+an NVT {\tt mdp} file with the target temperature set to what you
expect in your NVE simulation, and transfer the buffer size printed by
{\tt grompp} to your NVE {\tt mdp} file.
to SIMD units which can perform multiple floating operations at once
(e.g. SSE, AVX, CUDA on GPUs, BlueGene FPUs). These non-bonded kernels
are much faster than the kernels used in the group scheme for most
-types of systems, except for water molecules when not using a buffered
-pair list. This latter case is quite common for (bio-)molecular
-simulations, so for greatest speed, it is worth comparing the
-performance of both schemes.
+types of systems, except for water molecules on processors with short
+SIMD widths when not using a buffered pair list. This latter case is
+common for (bio-)molecular simulations, so for greatest speed, it is
+worth comparing the performance of both schemes.
As the Verlet cut-off scheme was introduced in version 4.6, not
all features of the group scheme are supported yet. The Verlet scheme
\dline
Non-bonded interaction feature & group & Verlet \\
\dline
-unbuffered cut-off scheme & $\surd$ & \\
+unbuffered cut-off scheme & $\surd$ & not by default \\
exact cut-off & shift/switch & $\surd$ \\
shifted interactions & force+energy & energy \\
-switched forces & $\surd$ & \\
+switched potential & $\surd$ & $\surd$ \\
+switched forces & $\surd$ & $\surd$ \\
non-periodic systems & $\surd$ & Z + walls \\
implicit solvent & $\surd$ & \\
-free energy perturbed non-bondeds & $\surd$ & \\
+free energy perturbed non-bondeds & $\surd$ & $\surd$ \\
group energy contributions & $\surd$ & CPU (not on GPU) \\
energy group exclusions & $\surd$ & \\
AdResS multi-scale & $\surd$ & \\
OpenMP multi-threading & only PME & $\surd$ \\
native GPU support & & $\surd$ \\
+Lennard-Jones PME & $\surd$ & $\surd$ \\
\dline
\end{tabular}
}
\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsubsection{Energy drift and pair-list buffering}
-For a canonical ensemble, the average energy error caused by the
+For a canonical (NVT) ensemble, the average energy error caused by the
finite Verlet buffer size can be determined from the atomic
displacements and the shape of the potential at the cut-off.
%Since we are interested in the small drift regime, we will assume
\subsubsection{Cut-off artifacts and switched interactions}
With the Verlet scheme, the pair potentials are shifted to be zero at
-the cut-off, such that the potential is the integral of the force.
-Note that in the group scheme this is not possible, because no exact
-cut-off distance is used. There can still be energy drift from
-non-zero forces at the cut-off. This effect is extremely small and
-often not noticeable, as other integration errors may dominate. To
+the cut-off, which makes the potential the integral of the force.
+This is only possible in the group scheme if the shape of the potential
+is such that its value is zero at the cut-off distance.
+However, there can still be energy drift when the
+forces are non-zero at the cut-off. This effect is extremely small and
+often not noticeable, as other integration errors (e.g. from constraints)
+may dominate. To
completely avoid cut-off artifacts, the non-bonded forces can be
switched exactly to zero at some distance smaller than the neighbor
list cut-off (there are several ways to do this in {\gromacs}, see
\secref{mod_nb_int}). One then has a buffer with the size equal to the
-neighbor list cut-off less the longest interaction cut-off. With the
-group cut-off scheme, one can then also choose to let {\tt mdrun} only
+neighbor list cut-off less the longest interaction cut-off.
+
+With the
+group cut-off scheme, one can also choose to let {\tt mdrun} only
update the neighbor list when required. That is when one or more
particles have moved more than half the buffer size from the center of
geometry of the \swapindex{charge}{group} to which they belong (see
cost, since the neighbor list update frequency will be determined by
just one or two particles moving slightly beyond the half buffer
length (which not even necessarily implies that the neighbor list is
-invalid), while 99.99\% of the particles are fine. } % Brace matches
-ifthenelse test for gmxlite
+invalid), while 99.99\% of the particles are fine.
+
+} % Brace matches ifthenelse test for gmxlite
\subsubsection{Simple search\swapindexquiet{simple}{search}}
Due to \eqnsref{box_rot}{simplerc}, the vector $\rvij$
out of the neighbor list. This reduces the cut-off effects from
the charge-charge level to the dipole-dipole level, which decay
much faster. With the advent of full range electrostatics methods,
-such as particle mesh Ewald (\secref{pme}), the use of charge groups is
+such as particle-mesh Ewald (\secref{pme}), the use of charge groups is
no longer required for accuracy. It might even have a slight negative effect
on the accuracy or efficiency, depending on how the neighbor list is made
and the interactions are calculated.
-But there is still an important reason for using ``charge groups'': efficiency.
+But there is still an important reason for using ``charge groups'': efficiency with the group cut-off scheme.
Where applicable, neighbor searching is carried out on the basis of
charge groups which are defined in the molecular topology.
If the nearest image distance between the {\em
this is relatively easy, as one can simply put hydrogen atoms, and in some
case oxygen atoms, in the same charge group as the heavy atom they
are connected to; for example: CH$_3$, CH$_2$, CH, NH$_2$, NH, OH, CO$_2$, CO.
+
+With the Verlet cut-off scheme, charge groups are ignored.
+
} % Brace matches ifthenelse test for gmxlite
\subsection{Compute forces}
\eeq
From this the absolute temperature $T$ can be computed using:
\beq
-\half N_{df} kT = E_{kin}
+\half N_{\mathrm{df}} kT = E_{\mathrm{kin}}
\label{eqn:E-T}
\eeq
where $k$ is Boltzmann's constant and $N_{df}$ is the number of
degrees of freedom which can be computed from:
\beq
-N_{df} ~=~ 3 N - N_c - N_{com}
+N_{\mathrm{df}} ~=~ 3 N - N_c - N_{\mathrm{com}}
\eeq
Here $N_c$ is the number of {\em \normindex{constraints}} imposed on the system.
-When performing molecular dynamics $N_{com}=3$ additional degrees of
+When performing molecular dynamics $N_{\mathrm{com}}=3$ additional degrees of
freedom must be removed, because the three
center-of-mass velocities are constants of the motion, which are usually
set to zero. When simulating in vacuo, the rotation around the center of mass
-can also be removed, in this case $N_{com}=6$.
+can also be removed, in this case $N_{\mathrm{com}}=6$.
When more than one temperature-coupling group\index{temperature-coupling group} is used, the number of degrees
of freedom for group $i$ is:
\beq
-N^i_{df} ~=~ (3 N^i - N^i_c) \frac{3 N - N_c - N_{com}}{3 N - N_c}
+N^i_{\mathrm{df}} ~=~ (3 N^i - N^i_c) \frac{3 N - N_c - N_{\mathrm{com}}}{3 N - N_c}
\eeq
The kinetic energy can also be written as a tensor, which is necessary
for pressure calculation in a triclinic system, or systems where shear
forces are imposed:
\beq
-{\bf E}_{kin} = \half \sum_i^N m_i \vvi \otimes \vvi
+{\bf E}_{\mathrm{kin}} = \half \sum_i^N m_i \vvi \otimes \vvi
\eeq
\subsubsection{Pressure and virial}
The \normindex{pressure}
tensor {\bf P} is calculated from the difference between
-kinetic energy $E_{kin}$ and the \normindex{virial} ${\bf \Xi}$:
+kinetic energy $E_{\mathrm{kin}}$ and the \normindex{virial} ${\bf \Xi}$:
\beq
-{\bf P} = \frac{2}{V} ({\bf E}_{kin}-{\bf \Xi})
+{\bf P} = \frac{2}{V} ({\bf E}_{\mathrm{kin}}-{\bf \Xi})
\label{eqn:P}
\eeq
where $V$ is the volume of the computational box.
a factor of 0.8. For 3-D domain decomposition this allows cells
to change their volume by about a factor of 0.5, which should allow
for compensation of a load imbalance of 100\%.
-The required scaling can be changed with the {\tt -dds} option of {\tt mdrun}.
+The minimum allowed scaling can be changed with the {\tt -dds}
+option of {\tt mdrun}.
\subsection{Constraints in parallel\index{constraints}}
\label{subsec:plincs}
\dline
interaction & range & option & default \\
\dline
-non-bonded & $r_c$ = max($r_{list}$,$r_{VdW}$,$r_{Coul}$) & {\tt mdp} file & \\
-two-body bonded & max($r_{mb}$,$r_c$) & {\tt mdrun -rdd} & starting conf. + 10\% \\
-multi-body bonded & $r_{mb}$ & {\tt mdrun -rdd} & starting conf. + 10\% \\
-constraints & $r_{con}$ & {\tt mdrun -rcon} & est. from bond lengths \\
-virtual sites & $r_{con}$ & {\tt mdrun -rcon} & 0 \\
+non-bonded & $r_c$ = max($r_{\mathrm{list}}$,$r_{\mathrm{VdW}}$,$r_{\mathrm{Coul}}$) & {\tt mdp} file & \\
+two-body bonded & max($r_{\mathrm{mb}}$,$r_c$) & {\tt mdrun -rdd} & starting conf. + 10\% \\
+multi-body bonded & $r_{\mathrm{mb}}$ & {\tt mdrun -rdd} & starting conf. + 10\% \\
+constraints & $r_{\mathrm{con}}$ & {\tt mdrun -rcon} & est. from bond lengths \\
+virtual sites & $r_{\mathrm{con}}$ & {\tt mdrun -rcon} & 0 \\
\dline
\end{tabular}
}
to stop with an error message of missing interactions.
The range for the bonded interactions is determined from the distance
between bonded charge-groups in the starting configuration, with 10\% added
-for headroom. For the constraints, the value of $r_{con}$ is determined by
+for headroom. For the constraints, the value of $r_{\mathrm{con}}$ is determined by
taking the maximum distance that ({\tt lincs_order + 1}) bonds can cover
when they all connect at angles of 120 degrees.
-The actual constraint communication is not limited by $r_{con}$,
+The actual constraint communication is not limited by $r_{\mathrm{con}}$,
but by the minimum cell size $L_C$, which has the following lower limit:
\beq
-L_C \geq \max(r_{mb},r_{con})
+L_C \geq \max(r_{\mathrm{mb}},r_{\mathrm{con}})
\eeq
Without dynamic load balancing the system is actually allowed to scale
beyond this limit when pressure scaling is used.
For rhombic dodecahedra this is a factor of $\sqrt{3/2}$ shorter
along $x$ and $y$.
-When $r_{mb} > r_c$, {\tt mdrun} employs a smart algorithm to reduce
+When $r_{\mathrm{mb}} > r_c$, {\tt mdrun} employs a smart algorithm to reduce
the communication. Simply communicating all charge groups within
-$r_{mb}$ would increase the amount of communication enormously.
+$r_{\mathrm{mb}}$ would increase the amount of communication enormously.
Therefore only charge-groups that are connected by bonded interactions
to charge groups which are not locally present are communicated.
This leads to little extra communication, but also to a slightly
increased cost for the domain decomposition setup.
In some cases, {\eg} coarse-grained simulations with a very short cut-off,
-one might want to set $r_{mb}$ by hand to reduce this cost.
+one might want to set $r_{\mathrm{mb}}$ by hand to reduce this cost.
\subsection{Multiple-Program, Multiple-Data PME parallelization\index{PME}}
\label{subsec:mpmd_pme}
generalized Born-formalism, and the Still~\cite{Still97}, HCT~\cite{Truhlar96},
and OBC~\cite{Case04} models are available for calculating the Born radii.
-Here, the free energy $G_{solv}$ of solvation is the sum of three terms,
-a solvent-solvent cavity term ($G_{cav}$), a solute-solvent van der
-Waals term ($G_{vdw}$), and finally a solvent-solute electrostatics
-polarization term ($G_{pol}$).
+Here, the free energy $G_{\mathrm{solv}}$ of solvation is the sum of three terms,
+a solvent-solvent cavity term ($G_{\mathrm{cav}}$), a solute-solvent van der
+Waals term ($G_{\mathrm{vdw}}$), and finally a solvent-solute electrostatics
+polarization term ($G_{\mathrm{pol}}$).
-The sum of $G_{cav}$ and $G_{vdw}$ corresponds to the (non-polar)
-free energy of solvation for a molecule from which all charges
-have been removed, and is commonly called $G_{np}$,
+The sum of $G_{\mathrm{cav}}$ and $G_{\mathrm{vdw}}$ corresponds to the (non-polar)
+free energy of solvation for a molecule from which all charges
+have been removed, and is commonly called $G_{\mathrm{np}}$,
calculated from the total solvent accessible surface area
multiplied with a surface tension.
The total expression for the solvation free energy then becomes:
\beq
-G_{solv} = G_{np} + G_{pol}
+G_{\mathrm{solv}} = G_{\mathrm{np}} + G_{\mathrm{pol}}
\label{eqn:gb_solv}
\eeq
-Under the generalized Born model, $G_{pol}$ is calculated from the generalized Born equation~\cite{Still97}:
+Under the generalized Born model, $G_{\mathrm{pol}}$ is calculated from the generalized Born equation~\cite{Still97}:
\beq
-G_{pol} = \left(1-\frac{1}{\epsilon}\right) \sum_{i=1}^n \sum_{j>i}^n \frac {q_i q_j}{\sqrt{r^2_{ij} + b_i b_j \exp\left(\frac{-r^2_{ij}}{4 b_i b_j}\right)}}
+G_{\mathrm{pol}} = \left(1-\frac{1}{\epsilon}\right) \sum_{i=1}^n \sum_{j>i}^n \frac {q_i q_j}{\sqrt{r^2_{ij} + b_i b_j \exp\left(\frac{-r^2_{ij}}{4 b_i b_j}\right)}}
\label{eqn:gb_still}
\eeq
In the end, the full re-formulation of~\ref{eqn:gb_still} becomes:
\beq
-G_{pol} = \left(1-\frac{1}{\epsilon}\right) \sum_{i=1}^n \sum_{j>i}^n \frac{q_i q_j}{\sqrt{b_i b_j}} ~\xi (x) = \left(1-\frac{1}{\epsilon}\right) \sum_{i=1}^n q_i c_i \sum_{j>i}^n q_j c_j~\xi (x)
+G_{\mathrm{pol}} = \left(1-\frac{1}{\epsilon}\right) \sum_{i=1}^n \sum_{j>i}^n \frac{q_i q_j}{\sqrt{b_i b_j}} ~\xi (x) = \left(1-\frac{1}{\epsilon}\right) \sum_{i=1}^n q_i c_i \sum_{j>i}^n q_j c_j~\xi (x)
\label{eqn:gb_final}
\eeq
-The non-polar part ($G_{np}$) of Equation~\ref{eqn:gb_solv} is calculated
+The non-polar part ($G_{\mathrm{np}}$) of Equation~\ref{eqn:gb_solv} is calculated
directly from the Born radius of each atom using a simple ACE type
approximation by Schaefer {\em et al.}~\cite{Karplus98}, including a
simple loop over all atoms.
See also \figref{shift}.
\begin{figure}
-\centerline{\includegraphics[angle=270,width=10cm]{plots/shiftf}}
+\centerline{\includegraphics[width=10cm]{plots/shiftf}}
\caption[The Coulomb Force, Shifted Force and Shift Function
$S(r)$,.]{The Coulomb Force, Shifted Force and Shift Function $S(r)$,
using r$_1$ = 2 and r$_c$ = 4.}
$i$ and $j$ is represented by a harmonic potential:
\begin{figure}
-\centerline{\raisebox{4cm}{\includegraphics[angle=270,width=5cm]{plots/bstretch}}\includegraphics[width=7cm]{plots/f-bond}}
+\centerline{\raisebox{2cm}{\includegraphics[width=5cm]{plots/bstretch}}\includegraphics[width=7cm]{plots/f-bond}}
\caption[Bond stretching.]{Principle of bond stretching (left), and the bond
stretching potential (right).}
\label{fig:bstretch1}
\ve{F}_i(\rvij) = k^b_{ij}(\rij^2-b_{ij}^2)~\rvij
\eeq
The force constants for this form of the potential are related to the usual
-harmonic force constant $k^{b,harm}$ (\secref{bondpot}) as
+harmonic force constant $k^{b,\mathrm{harm}}$ (\secref{bondpot}) as
\beq
-2 k^b b_{ij}^2 = k^{b,harm}
+2 k^b b_{ij}^2 = k^{b,\mathrm{harm}}
\eeq
The force constants are mostly derived from the harmonic ones used in
\gromosv{87}~\cite{biomos}. Although this form is computationally more
is also represented by a harmonic potential on the angle $\tijk$
\begin{figure}
-\centerline{\raisebox{4cm}{\includegraphics[angle=270,width=5cm]{plots/angle}}\includegraphics[width=7cm]{plots/f-angle}}
+\centerline{\raisebox{1cm}{\includegraphics[width=5cm]{plots/angle}}\includegraphics[width=7cm]{plots/f-angle}}
\caption[Angle vibration.]{Principle of angle vibration (left) and the
bond angle potential (right).}
\label{fig:angle}
\eeq
The corresponding force can be derived by partial differentiation with respect
to the atomic positions. The force constants in this function are related
-to the force constants in the harmonic form $k^{\theta,harm}$
+to the force constants in the harmonic form $k^{\theta,\mathrm{harm}}$
(\ssecref{harmonicangle}) by:
\beq
-k^{\theta} \sin^2(\tijk^0) = k^{\theta,harm}
+k^{\theta} \sin^2(\tijk^0) = k^{\theta,\mathrm{harm}}
\eeq
In the \gromosv{96} manual there is a much more complicated conversion formula
which is temperature dependent. The formulas are equivalent at 0 K
\normindex{mirror image}s, see \figref{imp}.
\begin {figure}
-\centerline{\includegraphics[angle=270,width=4cm]{plots/ring-imp}\hspace{1cm}
-\includegraphics[angle=270,width=3cm]{plots/subst-im}\hspace{1cm}\includegraphics[angle=270,width=3cm]{plots/tetra-im}}
+\centerline{\includegraphics[width=4cm]{plots/ring-imp}\hspace{1cm}
+\includegraphics[width=3cm]{plots/subst-im}\hspace{1cm}\includegraphics[width=3cm]{plots/tetra-im}}
\caption[Improper dihedral angles.]{Principle of improper
dihedral angles. Out of plane bending for rings (left), substituents
of rings (middle), out of tetrahedral (right). The improper dihedral
in the {\tt [ dihedraltypes ]} section.
\begin{figure}
-\centerline{\raisebox{4.5cm}{\includegraphics[angle=270,width=5cm]{plots/dih}}\includegraphics[width=7cm]{plots/f-dih}}
+\centerline{\raisebox{1cm}{\includegraphics[width=5cm]{plots/dih}}\includegraphics[width=7cm]{plots/f-dih}}
\caption[Proper dihedral angle.]{Principle of proper dihedral angle
(left, in {\em trans} form) and the dihedral angle potential (right).}
\label{fig:pdihf}
\begin{verbatim}
[ distance_restraints ]
-; ai aj type index type' low up1 up2 fac
+; ai aj type index type' low up1 up2 fac
10 16 1 0 1 0.0 0.3 0.4 1.0
10 28 1 1 1 0.0 0.3 0.4 1.0
10 46 1 1 1 0.0 0.3 0.4 1.0
sequentially, then the Coulombic interaction is turned off linearly,
rather than using soft core interactions, which should be less
statistically noisy in most cases. This behavior can be overwritten
-by using the mdp option {\tt sc-coul} to 'yes'. Additionally, the
+by using the mdp option {\tt sc-coul} to {\tt yes}. Additionally, the
soft-core interaction potential is only applied when either the A or B
state has zero interaction potential. If both A and B states have
nonzero interaction potential, default linear scaling described above
r_B &=& \left(\alpha \sigma_B^{48} \LL^p + r^{48} \right)^\frac{1}{48}
\eea
This ``1-1-48'' path is also implemented in {\gromacs}. Note that for this path the soft core $\alpha$
-should satisfy $0.001 < \alpha < 0.003$,rather than $\alpha \approx
+should satisfy $0.001 < \alpha < 0.003$, rather than $\alpha \approx
0.5$.
%} % Brace matches ifthenelse test for gmxlite
atoms {\bf i+1} and {\bf i+2} are called {\em \normindex{exclusions}} of atom {\bf i}.
\begin{figure}
-\centerline{\includegraphics[angle=270,width=8cm]{plots/chain}}
+\centerline{\includegraphics[width=8cm]{plots/chain}}
\caption{Atoms along an alkane chain.}
\label{fig:chain}
\end{figure}
the creation of charges, in which case you should consider using the
lattice sum methods provided by {\gromacs}.
-Consider a water molecule interacting with another atom. When we would apply
-the cut-off on an atom-atom basis we might include the atom-oxygen
+Consider a water molecule interacting with another atom. If we would apply
+a plain cut-off on an atom-atom basis we might include the atom-oxygen
interaction (with a charge of $-0.82$) without the compensating charge
of the protons, and as a result, induce a large dipole moment over the system.
Therefore, we have to keep groups of atoms with total charge
-0 together. These groups are called {\em charge groups}.
+0 together. These groups are called {\em charge groups}. Note that with
+a proper treatment of long-range electrostatics (e.g. particle-mesh Ewald
+(\secref{pme}), keeping charge groups together is not required.
-\subsection{Treatment of Cut-offs\index{cut-off}}
+\subsection{Treatment of Cut-offs in the group scheme\index{cut-off}}
\newcommand{\rs}{$r_{short}$}
\newcommand{\rl}{$r_{long}$}
{\gromacs} is quite flexible in treating cut-offs, which implies
slowly-converging sum \eqnref{totalcoulomb} into two
quickly-converging terms and a constant term:
\begin{eqnarray}
-V &=& V_{dir} + V_{rec} + V_{0} \\[0.5ex]
-V_{dir} &=& \frac{f}{2} \sum_{i,j}^{N}
+V &=& V_{\mathrm{dir}} + V_{\mathrm{rec}} + V_{0} \\[0.5ex]
+V_{\mathrm{dir}} &=& \frac{f}{2} \sum_{i,j}^{N}
\sum_{n_x}\sum_{n_y}
\sum_{n_{z}*} q_i q_j \frac{\mbox{erfc}(\beta {r}_{ij,{\bf n}} )}{{r}_{ij,{\bf n}}} \\[0.5ex]
-V_{rec} &=& \frac{f}{2 \pi V} \sum_{i,j}^{N} q_i q_j
+V_{\mathrm{rec}} &=& \frac{f}{2 \pi V} \sum_{i,j}^{N} q_i q_j
\sum_{m_x}\sum_{m_y}
\sum_{m_{z}*} \frac{\exp{\left( -(\pi {\bf m}/\beta)^2 + 2 \pi i
{\bf m} \cdot ({\bf r}_i - {\bf r}_j)\right)}}{{\bf m}^2} \\[0.5ex]
the Particle-mesh Ewald method as discussed for electrostatics above.
In this case the modified Ewald equations become
\begin{eqnarray}
-V &=& V_{dir} + V_{rec} + V_{0} \\[0.5ex]
-V_{dir} &=& -\frac{1}{2} \sum_{i,j}^{N}
+V &=& V_{\mathrm{dir}} + V_{\mathrm{rec}} + V_{0} \\[0.5ex]
+V_{\mathrm{dir}} &=& -\frac{1}{2} \sum_{i,j}^{N}
\sum_{n_x}\sum_{n_y}
\sum_{n_{z}*} \frac{C_{ij}^{(6)}g(\beta {r}_{ij,{\bf n}})}{{r_{ij,{\bf n}}}^6} \\[0.5ex]
-V_{rec} &=& \frac{{\pi}^{\frac{3}{2}} \beta^{3}}{2V} \sum_{m_x}\sum_{m_y}\sum_{m_{z}*}
+V_{\mathrm{rec}} &=& \frac{{\pi}^{\frac{3}{2}} \beta^{3}}{2V} \sum_{m_x}\sum_{m_y}\sum_{m_{z}*}
f(\pi |{\mathbf m}|/\beta) \times \sum_{i,j}^{N} C_{ij}^{(6)} {\mathrm{exp}}\left[-2\pi i {\bf m}\cdot({\bf r_i}-{\bf r_j})\right] \\[0.5ex]
V_{0} &=& -\frac{\beta^{6}}{12}\sum_{i}^{N} C_{ii}^{(6)},
\end{eqnarray}
all-atom parameters. That said, we describe the available options in
some detail.
-\subsection{GROMOS87\index{GROMOS87 force field}}
-The \gromosv{87} suite of programs and corresponding force
-field~\cite{biomos} formed the basis for the development of {\gromacs}
-in the early 1990s. The original GROMOS87 force field is not
-available in {\gromacs}. In previous versions ($<$ 3.3.2) there used
-to be the so-called ``{\gromacs} force field,'' which was based on
-\gromosv{87}~\cite{biomos}\index{GROMOS87}, with a small modification
-concerning the interaction between water oxygens and carbon
-atoms~\cite{Buuren93b,Mark94}, as well as 10 extra atom
-types~\cite{Jorgensen83,Buuren93a,Buuren93b,Mark94,Liu95}.
-
-Since version 5.0 this force field has been ``deprecated''. Should
-you have a justifiable reason to use this force field please
-use eariler versions of {\gromacs}.
-
\subsubsection{All-hydrogen force field}
The \gromosv{87}-based all-hydrogen force field is almost identical to the
normal \gromosv{87} force field, since the extra hydrogens have no
\subsection{AMBER\index{AMBER force field}}
-As of version 4.5, {\gromacs} provides native support for the following AMBER force fields:
+{\gromacs} provides native support for the following AMBER force fields:
\begin{itemize}
\item AMBER94~\cite{Cornell1995}
\subsection{CHARMM\index{CHARMM force field}}
\label{subsec:charmmff}
-As of version 4.5, {\gromacs} supports the CHARMM27 force field for proteins~\cite{mackerell04, mackerell98}, lipids~\cite{feller00} and nucleic acids~\cite{foloppe00}. The protein parameters (and to some extent the lipid and nucleic acid parameters) were thoroughly tested -- both by comparing potential energies between the port and the standard parameter set in the CHARMM molecular simulation package, as well by how the protein force field behaves together with {\gromacs}-specific techniques such as virtual sites (enabling long time steps) and a fast implicit solvent recently implemented~\cite{Larsson10} -- and the details and results are presented in the paper by Bjelkmar et al.~\cite{Bjelkmar10}. The nucleic acid parameters, as well as the ones for HEME, were converted and tested by Michel Cuendet.
+{\gromacs} supports the CHARMM force field for proteins~\cite{mackerell04, mackerell98}, lipids~\cite{feller00} and nucleic acids~\cite{foloppe00,Mac2000}. The protein parameters (and to some extent the lipid and nucleic acid parameters) were thoroughly tested -- both by comparing potential energies between the port and the standard parameter set in the CHARMM molecular simulation package, as well by how the protein force field behaves together with {\gromacs}-specific techniques such as virtual sites (enabling long time steps) and a fast implicit solvent recently implemented~\cite{Larsson10} -- and the details and results are presented in the paper by Bjelkmar et al.~\cite{Bjelkmar10}. The nucleic acid parameters, as well as the ones for HEME, were converted and tested by Michel Cuendet.
When selecting the CHARMM force field in {\tt \normindex{pdb2gmx}} the default option is to use \normindex{CMAP} (for torsional correction map). To exclude CMAP, use {\tt -nocmap}. The basic form of the CMAP term implemented in {\gromacs} is a function of the $\phi$ and $\psi$ backbone torsion angles. This term is defined in the {\tt .rtp} file by a {\tt [ cmap ]} statement at the end of each residue supporting CMAP. The following five atom names define the two torsional angles. Atoms 1-4 define $\phi$, and atoms 2-5 define $\psi$. The corresponding atom types are then matched to the correct CMAP type in the {\tt cmap.itp} file that contains the correction maps.
+A port of the CHARMM36 force field for use with GROMACS is also available at \url{http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs}.
+
\subsection{Coarse-grained force-fields}
\index{force-field, coarse-grained}
\label{sec:cg-forcefields}
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013, by the GROMACS development team, led by
+% Copyright (c) 2013,2014, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
It is clear that only one iteration extra (in double
precision) is needed for a double-precision result.
-\section{Modifying GROMACS}
-The following files have to be edited in case you want to add a bonded
-potential of any type.
-\begin{enumerate}
-\item {\tt include/bondf.h}
-\item {\tt include/types/idef.h}
-\item {\tt include/types/nrnb.h}
-\item {\tt include/types/enums.h}
-\item {\tt include/grompp.h}
-\item {\tt src/kernel/topdirs.c}
-\item {\tt src/gmxlib/tpxio.c}
-\item {\tt src/gmxlib/bondfree.c}
-\item {\tt src/gmxlib/ifunc.c}
-\item {\tt src/gmxlib/nrnb.c}
-\item {\tt src/kernel/convparm.c}
-\item {\tt src/kernel/topdirs.c}
-\item {\tt src/kernel/topio.c}
-\end{enumerate}
-
% LocalWords: Virial virial triclinic intra mol mshift shiftvec sqrt SPC lj yf
% LocalWords: coul Fortran SGI AMD Raphson IEEE taylor epsr accy ieee yx fpdef
% LocalWords: lsb nr inversef src formulae GROMACS
pages = {2887--2899},
year = 2013
}
+
+@article {Mac2000,
+author = {MacKerell, Alexander D. and Banavali, Nilesh K.},
+title = {All-atom empirical force field for nucleic acids: {II.} Application to molecular dynamics simulations of {DNA} and {RNA} in solution},
+journal = BTjcc,
+volume = {21},
+number = {2},
+publisher = {John Wiley & Sons, Inc.},
+issn = {1096-987X},
+url = {http://dx.doi.org/10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P},
+doi = {10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P},
+pages = {105--120},
+keywords = {CHARMM, force field, molecular dynamics, parametrization, DNA, RNA},
+year = {2000},
+}
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\newcommand{\ttss}{\tt \scriptsize}
\begin{landscape}
-\begin{longtable}{|l|lcc>{\raggedright}p{2.5in}cc|}
+\begin{longtable}{|p{1.8in}|lcc>{\raggedright}p{2.5in}cc|}
\caption{Details of {\tt [~moleculetype~]} directives}\\
\dline
Name of interaction & Topology file directive & num. & func. & Order of parameters and their units & use in & Cross- \\
\endhead
\dline
\endfoot
-\label{tab:topfile2}\footnotetext[1]{The required number of atom indices for this directive}\footnotetext[2]{The index to use to select this function type}\footnotetext[3]{Indicates which of the parameters for this interaction can be interpolated during free energy calculations}\footnotetext[4]{This interaction type will be used by {{\tts grompp}} for generating exclusions}\footnotetext[5]{This interaction type can be converted to constraints by {{\tts grompp}}}\footnotetext[7]{The combination rule determines the type of LJ parameters, see~\ssecref{nbpar}}\footnotetext[6]{No connection, and so no exclusions, are generated for this interaction}bond
- & {\tts bonds}\fnm{4},\fnm{5} & 2 & 1 & $b_0$ (nm); $k_b$ (\kJmolnm{-2}) & all & \ssecref{harmonicbond} \\
+% The footnotetext fields only work inside the body, and not from a
+% column with ``p'' formatting'!
+bond & {\tts bonds}\fnm{4},\fnm{5} & 2 & 1 & $b_0$ (nm); $k_b$ (\kJmolnm{-2}) & all & \ssecref{harmonicbond}
+\label{tab:topfile2} \footnotetext[1]{The required number of atom indices for this directive}\footnotetext[2]{The index to use to select this function type}\footnotetext[3]{Indicates which of the parameters for this interaction can be interpolated during free energy calculations}\footnotetext[4]{This interaction type will be used by {{\tts grompp}} for generating exclusions}\footnotetext[5]{This interaction type can be converted to constraints by {{\tts grompp}}}\footnotetext[7]{The combination rule determines the type of LJ parameters, see~\ssecref{nbpar}}\footnotetext[6]{No connection, and so no exclusions, are generated for this interaction}
+\\
G96 bond & {\tts bonds}\fnm{4},\fnm{5} & 2 & 2 & $b_0$ (nm); $k_b$ (\kJmolnm{-4}) & all & \ssecref{G96bond} \\
Morse & {\tts bonds}\fnm{4},\fnm{5} & 2 & 3 & $b_0$ (nm); $D$ (\kJmol); $\beta$ (nm$^{-1}$) & all & \ssecref{Morsebond} \\
cubic bond & {\tts bonds}\fnm{4},\fnm{5} & 2 & 4 & $b_0$ (nm); $C_{i=2,3}$ (\kJmolnm{-i}) & & \ssecref{cubicbond} \\
\label{subsec:fffiles}
Many force fields are available by default.
Force fields are detected by the presence of {\tt <name>.ff} directories
-in the {\gromacs} {\tt /share/top} sub-directory and/or the working directory.
+in the {\tt \$GMXLIB/share/gromacs/top} sub-directory and/or the working directory.
The information regarding the location of the force field files is printed
by {\tt pdb2gmx} so you can easily keep track of which version of a force field
is being called, in case you have made modifications in one location or another.
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff