我对你的代码做了一些小改动。
1.我调用了SwingUtilitiesinvokeLater方法来启动应用程序。此方法确保Swing组件在Event Dispatch Thread上创建和执行。
1.我将simulationFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);移动到了正确的位置。JFrame方法必须以特定的顺序调用。
1.我降低了点的速度。如果你想要平滑的运动，你应该在一个时间段内只移动像素或像素的分数。为了弥补速度较慢，我降低了摆动Timer时间。最小摆动Timer时间是5毫秒。
下面是完整的可运行代码。我把你的附加类放在内部类中，这样我就可以把代码编译、运行和发布为一个块。

import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;

import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.SwingUtilities;
import javax.swing.Timer;

public class SimulationFrame {

    public SimulationFrame() {
        JFrame simulationFrame = new JFrame();
        simulationFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        simulationFrame.setContentPane(new SimulationPanel());
        simulationFrame.pack();
        simulationFrame.setLocation(0, 0);
        simulationFrame.setVisible(true);
    }

    public static void main(String[] args) {
        SwingUtilities.invokeLater(new Runnable() {
            @Override
            public void run() {
                new SimulationFrame();
            }
        });
    }

    public class SimulationPanel extends JPanel implements ActionListener {

        private static final long serialVersionUID = 1L;

        public ArrayList<Point> listPoints = new ArrayList<Point>();

        private int width = 1000;
        private int height = 1000;

        public SimulationPanel() {

            Point p1 = new Point(10, 10);
            Point p2 = new Point(20, 20);
            Point p3 = new Point(30, 30);

            p1.modify_speed(2, 1);
            p2.modify_speed(1, 2);
            p3.modify_speed(2, 2);

            listPoints.add(p1);
            listPoints.add(p2);
            listPoints.add(p3);
            setPreferredSize(new Dimension(width, height));
            Timer timer = new Timer(20, this);
            timer.start();
        }

        public void actionPerformed(ActionEvent e) {
            if (e.getSource() instanceof Timer) {
                for (Point p : listPoints) {
                    p.add_position(p.get_speed()[0], p.get_speed()[1]);
                }
                repaint();
            }
        }

        @Override
        public void paintComponent(Graphics g) {
            super.paintComponent(g);
            Graphics2D g2 = (Graphics2D) g.create();
            g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                    RenderingHints.VALUE_ANTIALIAS_ON);
            g2.setColor(java.awt.Color.RED);
            for (Point p : listPoints) {
                g2.fillOval(p.get_position()[0], p.get_position()[1], 10, 10);
            }
            g2.dispose();
        }
    }

    public class Point {

        private int x;
        private int y;
        private int[] speed = new int[2];

        public Point(int x, int y) {
            this.x = x;
            this.y = y;
        }

        public int[] get_position() {
            return new int[] { this.x, this.y };
        }

        public int[] get_speed() {
            return this.speed;
        }

        public void modify_position(int x, int y) {
            this.x = x;
            this.y = y;
        }

        public void modify_speed(int speed_x, int speed_y) {
            this.speed[0] = speed_x;
            this.speed[1] = speed_y;
        }

        public void add_position(int speed_x, int speed_y) {
            this.x += speed_x;
            this.y += speed_y;
        }
    }
}