315 |
|
isolated and conserve energy, Microcanonical ensemble(NVE) has a |
316 |
|
partition function like, |
317 |
|
\begin{equation} |
318 |
< |
\Omega (N,V,E) = e^{\beta TS} |
319 |
< |
\label{introEqaution:NVEPartition}. |
318 |
> |
\Omega (N,V,E) = e^{\beta TS} \label{introEquation:NVEPartition}. |
319 |
|
\end{equation} |
320 |
|
A canonical ensemble(NVT)is an ensemble of systems, each of which |
321 |
|
can share its energy with a large heat reservoir. The distribution |
634 |
|
Let $\varphi$ be the flow of Hamiltonian vector field, $\varphi$ is |
635 |
|
a \emph{symplectic} flow if it satisfies, |
636 |
|
\begin{equation} |
637 |
< |
'\varphi^T J '\varphi = J. |
637 |
> |
{\varphi '}^T J \varphi ' = J. |
638 |
|
\end{equation} |
639 |
|
According to Liouville's theorem, the symplectic volume is invariant |
640 |
|
under a Hamiltonian flow, which is the basis for classical |
642 |
|
field on a symplectic manifold can be shown to be a |
643 |
|
symplectomorphism. As to the Poisson system, |
644 |
|
\begin{equation} |
645 |
< |
'\varphi ^T J '\varphi = J \circ \varphi |
645 |
> |
{\varphi '}^T J \varphi ' = J \circ \varphi |
646 |
|
\end{equation} |
647 |
|
is the property must be preserved by the integrator. |
648 |
|
|
660 |
|
In other words, the flow of this vector field is reversible if and |
661 |
|
only if $ h \circ \varphi ^{ - 1} = \varphi \circ h $. |
662 |
|
|
663 |
< |
When designing any numerical methods, one should always try to |
663 |
> |
A \emph{first integral}, or conserved quantity of a general |
664 |
> |
differential function is a function $ G:R^{2d} \to R^d $ which is |
665 |
> |
constant for all solutions of the ODE $\frac{{dx}}{{dt}} = f(x)$ , |
666 |
> |
\[ |
667 |
> |
\frac{{dG(x(t))}}{{dt}} = 0. |
668 |
> |
\] |
669 |
> |
Using chain rule, one may obtain, |
670 |
> |
\[ |
671 |
> |
\sum\limits_i {\frac{{dG}}{{dx_i }}} f_i (x) = f \bullet \nabla G, |
672 |
> |
\] |
673 |
> |
which is the condition for conserving \emph{first integral}. For a |
674 |
> |
canonical Hamiltonian system, the time evolution of an arbitrary |
675 |
> |
smooth function $G$ is given by, |
676 |
> |
\begin{equation} |
677 |
> |
\begin{array}{c} |
678 |
> |
\frac{{dG(x(t))}}{{dt}} = [\nabla _x G(x(t))]^T \dot x(t) \\ |
679 |
> |
= [\nabla _x G(x(t))]^T J\nabla _x H(x(t)). \\ |
680 |
> |
\end{array} |
681 |
> |
\label{introEquation:firstIntegral1} |
682 |
> |
\end{equation} |
683 |
> |
Using poisson bracket notion, Equation |
684 |
> |
\ref{introEquation:firstIntegral1} can be rewritten as |
685 |
> |
\[ |
686 |
> |
\frac{d}{{dt}}G(x(t)) = \left\{ {G,H} \right\}(x(t)). |
687 |
> |
\] |
688 |
> |
Therefore, the sufficient condition for $G$ to be the \emph{first |
689 |
> |
integral} of a Hamiltonian system is |
690 |
> |
\[ |
691 |
> |
\left\{ {G,H} \right\} = 0. |
692 |
> |
\] |
693 |
> |
As well known, the Hamiltonian (or energy) H of a Hamiltonian system |
694 |
> |
is a \emph{first integral}, which is due to the fact $\{ H,H\} = |
695 |
> |
0$. |
696 |
> |
|
697 |
> |
|
698 |
> |
When designing any numerical methods, one should always try to |
699 |
|
preserve the structural properties of the original ODE and its flow. |
700 |
|
|
701 |
|
\subsection{\label{introSection:constructionSymplectic}Construction of Symplectic Methods} |
719 |
|
ordinary implicit Runge-Kutta methods are not suitable for |
720 |
|
Hamiltonian system. Recently, various high-order explicit |
721 |
|
Runge--Kutta methods have been developed to overcome this |
722 |
< |
instability \cite{}. However, due to computational penalty involved |
723 |
< |
in implementing the Runge-Kutta methods, they do not attract too |
724 |
< |
much attention from Molecular Dynamics community. Instead, splitting |
725 |
< |
have been widely accepted since they exploit natural decompositions |
726 |
< |
of the system\cite{Tuckerman92}. |
722 |
> |
instability. However, due to computational penalty involved in |
723 |
> |
implementing the Runge-Kutta methods, they do not attract too much |
724 |
> |
attention from Molecular Dynamics community. Instead, splitting have |
725 |
> |
been widely accepted since they exploit natural decompositions of |
726 |
> |
the system\cite{Tuckerman92}. |
727 |
|
|
728 |
|
\subsubsection{\label{introSection:splittingMethod}Splitting Method} |
729 |
|
|
770 |
|
splitting gives a second-order decomposition, |
771 |
|
\begin{equation} |
772 |
|
\varphi _h = \varphi _{1,h/2} \circ \varphi _{2,h} \circ \varphi |
773 |
< |
_{1,h/2} , |
740 |
< |
\label{introEqaution:secondOrderSplitting} |
773 |
> |
_{1,h/2} , \label{introEquation:secondOrderSplitting} |
774 |
|
\end{equation} |
775 |
|
which has a local error proportional to $h^3$. Sprang splitting's |
776 |
|
popularity in molecular simulation community attribute to its |
777 |
|
symmetric property, |
778 |
|
\begin{equation} |
779 |
|
\varphi _h^{ - 1} = \varphi _{ - h}. |
780 |
< |
\lable{introEquation:timeReversible} |
780 |
> |
\label{introEquation:timeReversible} |
781 |
|
\end{equation} |
782 |
|
|
783 |
|
\subsubsection{\label{introSection:exampleSplittingMethod}Example of Splitting Method} |
835 |
|
\frac{{\Delta t}}{{2m}}\dot q(0)} \right], % |
836 |
|
\label{introEquation:positionVerlet1} \\% |
837 |
|
% |
838 |
< |
q(\Delta t) = q(0) + \frac{{\Delta t}}{2}\left[ {\dot q(0) + \dot |
838 |
> |
q(\Delta t) &= q(0) + \frac{{\Delta t}}{2}\left[ {\dot q(0) + \dot |
839 |
|
q(\Delta t)} \right]. % |
840 |
|
\label{introEquation:positionVerlet1} |
841 |
|
\end{align} |
861 |
|
\] |
862 |
|
Applying Baker-Campbell-Hausdorff formula to Sprang splitting, we |
863 |
|
can obtain |
864 |
< |
\begin{eqnarray} |
864 |
> |
\begin{eqnarray*} |
865 |
|
\exp (h X/2)\exp (h Y)\exp (h X/2) & = & \exp (h X + h Y + h^2 |
866 |
< |
[X,Y]/4 + h^2 [Y,X]/4 \\ & & \mbox{} + h^2 [X,X]/8 + h^2 [Y,Y]/8 + |
867 |
< |
h^3 [Y,[Y,X]]/12 - h^3 [X,[X,Y]]/24 + \ldots ) |
868 |
< |
\end{eqnarray} |
866 |
> |
[X,Y]/4 + h^2 [Y,X]/4 \\ & & \mbox{} + h^2 [X,X]/8 + h^2 [Y,Y]/8 \\ |
867 |
> |
& & \mbox{} + h^3 [Y,[Y,X]]/12 - h^3 [X,[X,Y]]/24 & & \mbox{} + |
868 |
> |
\ldots ) |
869 |
> |
\end{eqnarray*} |
870 |
|
Since \[ [X,Y] + [Y,X] = 0\] and \[ [X,X] = 0\], the dominant local |
871 |
|
error of Spring splitting is proportional to $h^3$. The same |
872 |
|
procedure can be applied to general splitting, of the form |
905 |
|
|
906 |
|
\subsection{\label{introSec:mdInit}Initialization} |
907 |
|
|
908 |
+ |
\subsection{\label{introSec:forceEvaluation}Force Evaluation} |
909 |
+ |
|
910 |
|
\subsection{\label{introSection:mdIntegration} Integration of the Equations of Motion} |
911 |
|
|
912 |
|
\section{\label{introSection:rigidBody}Dynamics of Rigid Bodies} |
913 |
|
|
914 |
< |
A rigid body is a body in which the distance between any two given |
915 |
< |
points of a rigid body remains constant regardless of external |
916 |
< |
forces exerted on it. A rigid body therefore conserves its shape |
917 |
< |
during its motion. |
918 |
< |
|
919 |
< |
Applications of dynamics of rigid bodies. |
914 |
> |
Rigid bodies are frequently involved in the modeling of different |
915 |
> |
areas, from engineering, physics, to chemistry. For example, |
916 |
> |
missiles and vehicle are usually modeled by rigid bodies. The |
917 |
> |
movement of the objects in 3D gaming engine or other physics |
918 |
> |
simulator is governed by the rigid body dynamics. In molecular |
919 |
> |
simulation, rigid body is used to simplify the model in |
920 |
> |
protein-protein docking study{\cite{Gray03}}. |
921 |
|
|
922 |
+ |
It is very important to develop stable and efficient methods to |
923 |
+ |
integrate the equations of motion of orientational degrees of |
924 |
+ |
freedom. Euler angles are the nature choice to describe the |
925 |
+ |
rotational degrees of freedom. However, due to its singularity, the |
926 |
+ |
numerical integration of corresponding equations of motion is very |
927 |
+ |
inefficient and inaccurate. Although an alternative integrator using |
928 |
+ |
different sets of Euler angles can overcome this difficulty\cite{}, |
929 |
+ |
the computational penalty and the lost of angular momentum |
930 |
+ |
conservation still remain. A singularity free representation |
931 |
+ |
utilizing quaternions was developed by Evans in 1977. Unfortunately, |
932 |
+ |
this approach suffer from the nonseparable Hamiltonian resulted from |
933 |
+ |
quaternion representation, which prevents the symplectic algorithm |
934 |
+ |
to be utilized. Another different approach is to apply holonomic |
935 |
+ |
constraints to the atoms belonging to the rigid body. Each atom |
936 |
+ |
moves independently under the normal forces deriving from potential |
937 |
+ |
energy and constraint forces which are used to guarantee the |
938 |
+ |
rigidness. However, due to their iterative nature, SHAKE and Rattle |
939 |
+ |
algorithm converge very slowly when the number of constraint |
940 |
+ |
increases. |
941 |
+ |
|
942 |
+ |
The break through in geometric literature suggests that, in order to |
943 |
+ |
develop a long-term integration scheme, one should preserve the |
944 |
+ |
symplectic structure of the flow. Introducing conjugate momentum to |
945 |
+ |
rotation matrix $A$ and re-formulating Hamiltonian's equation, a |
946 |
+ |
symplectic integrator, RSHAKE, was proposed to evolve the |
947 |
+ |
Hamiltonian system in a constraint manifold by iteratively |
948 |
+ |
satisfying the orthogonality constraint $A_t A = 1$. An alternative |
949 |
+ |
method using quaternion representation was developed by Omelyan. |
950 |
+ |
However, both of these methods are iterative and inefficient. In |
951 |
+ |
this section, we will present a symplectic Lie-Poisson integrator |
952 |
+ |
for rigid body developed by Dullweber and his coworkers\cite{}. |
953 |
+ |
|
954 |
|
\subsection{\label{introSection:lieAlgebra}Lie Algebra} |
955 |
|
|
956 |
+ |
\subsection{\label{introSection:constrainedHamiltonianRB}Constrained Hamiltonian for Rigid Body} |
957 |
+ |
|
958 |
+ |
\begin{equation} |
959 |
+ |
H = \frac{1}{2}(p^T m^{ - 1} p) + \frac{1}{2}tr(PJ^{ - 1} P) + |
960 |
+ |
V(q,Q) + \frac{1}{2}tr[(QQ^T - 1)\Lambda ]. |
961 |
+ |
\label{introEquation:RBHamiltonian} |
962 |
+ |
\end{equation} |
963 |
+ |
Here, $q$ and $Q$ are the position and rotation matrix for the |
964 |
+ |
rigid-body, $p$ and $P$ are conjugate momenta to $q$ and $Q$ , and |
965 |
+ |
$J$, a diagonal matrix, is defined by |
966 |
+ |
\[ |
967 |
+ |
I_{ii}^{ - 1} = \frac{1}{2}\sum\limits_{i \ne j} {J_{jj}^{ - 1} } |
968 |
+ |
\] |
969 |
+ |
where $I_{ii}$ is the diagonal element of the inertia tensor. This |
970 |
+ |
constrained Hamiltonian equation subjects to a holonomic constraint, |
971 |
+ |
\begin{equation} |
972 |
+ |
Q^T Q = 1$, \label{introEquation:orthogonalConstraint} |
973 |
+ |
\end{equation} |
974 |
+ |
which is used to ensure rotation matrix's orthogonality. |
975 |
+ |
Differentiating \ref{introEquation:orthogonalConstraint} and using |
976 |
+ |
Equation \ref{introEquation:RBMotionMomentum}, one may obtain, |
977 |
+ |
\begin{equation} |
978 |
+ |
Q^t PJ^{ - 1} + J^{ - 1} P^t Q = 0 . \\ |
979 |
+ |
\label{introEquation:RBFirstOrderConstraint} |
980 |
+ |
\end{equation} |
981 |
+ |
|
982 |
+ |
Using Equation (\ref{introEquation:motionHamiltonianCoordinate}, |
983 |
+ |
\ref{introEquation:motionHamiltonianMomentum}), one can write down |
984 |
+ |
the equations of motion, |
985 |
+ |
\[ |
986 |
+ |
\begin{array}{c} |
987 |
+ |
\frac{{dq}}{{dt}} = \frac{p}{m} \label{introEquation:RBMotionPosition}\\ |
988 |
+ |
\frac{{dp}}{{dt}} = - \nabla _q V(q,Q) \label{introEquation:RBMotionMomentum}\\ |
989 |
+ |
\frac{{dQ}}{{dt}} = PJ^{ - 1} \label{introEquation:RBMotionRotation}\\ |
990 |
+ |
\frac{{dP}}{{dt}} = - \nabla _q V(q,Q) - 2Q\Lambda . \label{introEquation:RBMotionP}\\ |
991 |
+ |
\end{array} |
992 |
+ |
\] |
993 |
+ |
|
994 |
+ |
|
995 |
+ |
\[ |
996 |
+ |
M = \left\{ {(Q,P):Q^T Q = 1,Q^t PJ^{ - 1} + J^{ - 1} P^t Q = 0} |
997 |
+ |
\right\} . |
998 |
+ |
\] |
999 |
+ |
|
1000 |
|
\subsection{\label{introSection:DLMMotionEquation}The Euler Equations of Rigid Body Motion} |
1001 |
|
|
1002 |
< |
\subsection{\label{introSection:otherRBMotionEquation}Other Formulations for Rigid Body Motion} |
1002 |
> |
\subsection{\label{introSection:symplecticDiscretizationRB}Symplectic Discretization of Euler Equations} |
1003 |
|
|
891 |
– |
\section{\label{introSection:correlationFunctions}Correlation Functions} |
1004 |
|
|
1005 |
|
\section{\label{introSection:langevinDynamics}Langevin Dynamics} |
1006 |
|
|
1209 |
|
|
1210 |
|
\subsection{\label{introSection:centersRigidBody}Centers of Rigid |
1211 |
|
Body} |
1212 |
+ |
|
1213 |
+ |
\section{\label{introSection:correlationFunctions}Correlation Functions} |