Simulating a Pendulum with “Animate” and “True” Graphics:

ClearAll["Global`*"];

g=9.8;          (* gravitational acceleration in m/(s^2)*)
len=1;          (* length of pendulum arm, in meters*)
rb=0.05;     (* radius for drawing of ball, as fraction of length *)
period=2*π*(Sqrt[(len/g)]);      (* calculate period in seconds *)
amplitude = 0.5 ;                (* Initial amplitude or displacement, in radians *)
duration=4*period;         (* Duration of the animation *)
ϕ[t_]:=amplitude Cos[((2 π t)/period)]; (* angular position as a function of time *)

Setting up the Animation
We usually make a sketch (e.g., in Word) to show my coordinates, scales, origin, boundaries, and so on. 
The blue line is "len", and I decided to "zoom in" on the pendulum in the following way. I made these choices so 
that the pendulum uses most of the image space without the bob moving out of the image space.
You could easily make other choices. Also note that I explicitly showed the (x, y) coordinate system to myself!
Specifically, the bob is at the origin when the string is straight down.

Using "Graphics" Commands
Summary of the Graphics Commands used below:
I am drawing two "objects": a blue LINE and a red POINT (the circle). 
The adjectives preceding  "Line" (thin, blue) are obvious. The word "Line" is followed by 4 numbers, in two pairs:
     {0,len} refers to the {x,y} coordinates at the TOP of the pendulum.   The next pair are the {x,y} coordinates for the bob as a function of time. 
     
The  adjectives preceding "Point" (pointsize, Red) are also obvious. 
       {x, y} refers to the location of this Point, and it is obvious that the Point is at the same position as the bottom of the earlier blue line.
 
 In this group of two "graphics", drawings are added in the order listed. As a result, the red "point" is ON TOP of the blue line. 
  If you switched the order, you would see the blue line extend to the CENTER of the red ball, whereas in this version,
    the blue line extends under the red ball to its center.
Besides "Line" and "Point", some other options are: Rectangle, Polygon, Circle, and Disc.
Point, Circle, and Disc are all similar. Circle is hollow, but Disc is filled with some color.

plotbob[tmax_]:=Animate[Graphics[{{Thin,Blue,Line[{{0,len},{len*Sin[ϕ[t]],len*(1-Cos[ϕ[t]])}}]},{PointSize[rb/len],Red,Point[{len Sin[ϕ[t]],len (1-Cos[ϕ[t]])}]}},Frame->False, PlotRange ->{{-len,len},{-.25 len,1.25len}}],{t,0,tmax}]

The ANIMATE command generates all the animation frames, but doesn't show them. That happens below...
You can't use "Manipulate" for this because it's not a plot, it's a drawing made with a "Graphics" command.
In this version, I'm not bothering to save the movie to an external file. But, see the next demo...

pendplot=plotbob[duration] (* this line SHOWS the animation here in Mathematica*)