\documentclass{article}

\usepackage[margin=1in]{geometry}% Just for this example
\usepackage{amsmath}

\begin{document}

\begin{equation}\label{en:Moves1}
  \begin{aligned}
    &\textnormal{1. An MD trajectory of the $D$ real particles while one of them is removed.} \\
    &\textnormal{\parbox{.9\textwidth}{%
      2. An MD trajectory of the $D$ real particles while a new particle is inserted making a reservoir particle become real.}} \\
    &\textnormal{3. An MD trajectory of the $D$ real particles.}
  \end{aligned}
\end{equation}

\begin{equation}\label{en:Moves2}
  \begin{aligned}
    1.~&\textnormal{An MD trajectory of the $D$ real particles while one of them is removed.} \\
    2.~&\parbox[t]{.9\textwidth}{\raggedright
      An MD trajectory of the $D$ real particles while a new particle is inserted making a reservoir particle become real.} \\
    3.~&\textnormal{An MD trajectory of the $D$ real particles.}
  \end{aligned}
\end{equation}

\end{document}