Basic Java dice game
Your main() function desperately needs to be busted up, for multiple reasons:


You use a lot of variables, all of them declared at the top of main().  A human mind is only good at keeping track of about 7 things at a time, so this code is hard to follow.
It violates the Single Responsibility Principle, by parsing the command line, throwing the dice, keeping the statistics, and printing the report.  That's a lot of work for one function!
Object-oriented code is preferred in Java.  A static function avoids object-oriented thinking.
It's unclear what you're simulating: what constitutes a trial, and what you mean by biggest/smallest sum.




A quick win in readability can be obtained by defining a Die class: die.toss() reads like English, whereas 1 + (int) ((Math.random() * (6 - 1)) + 1) doesn't.

class Die {
    // Since "throw" is a Java keyword, we use "toss"
    int toss() {
        return 1 + (int)(6 * Math.random());
    }
}




A good start to taming the variables would be to declare each of them in the tightest scope possible.  For example, theSum, and diceSum are only relevant inside the loop.  count is a loop counter, and it's much easier to recognize if you rewrite the loop as a for-loop.  dice1 and dice2 are only relevant inside the inner loop, which is better expressed as a do-while loop.

for (int count = 0; count &lt; Integer.parseInt(args[0]); count++) {
    int theSum = 0, diceSum;
    do {
        int dice1 = 1 + (int) ((Math.random() * (6 - 1)) + 1);
        int dice2 = 1 + (int) ((Math.random() * (6 - 1)) + 1);
        diceSum = dice1 + dice2;
        if (diceSum != 7) {
            theSum = theSum + diceSum;
        }
        //System.out.println("the sum is "+theSum);
    } while (diceSum != 7);
    …
}


Now a picture is beginning to emerge.  The inner loop is what you would call a simulation trial.  Based on that, I would define a DiceSimulation class with a runTrial() method.  Everything else just falls into place around that core function.  ☺

public class DiceSimulation {
    private int trials = 0,                 // Formerly count
                min = Integer.MAX_VALUE,    // Formerly lowest
                max = 0,                    // Formerly finalSum
                sum = 0;                    // Formerly totalSum

    private Die die1 = new Die(),
                die2 = new Die();

    /**
     * One trial consists of tossing a pair of dice until a sum of 7 is obtained.
     * The result of the trial is the sum of all tosses up to, but not including,
     * the toss that resulted in 7.
     */
    public int runTrial() {
        int trialSum = 0, pairSum;           // Formerly theSum and diceSum
        while (7 != (pairSum = die1.toss() + die2.toss())) {
            trialSum += pairSum;
        }

        if (trialSum &gt; max) {
            max = trialSum;
        }
        if (trialSum &lt; min) {
            min = trialSum;
        }
        sum += trialSum;
        trials++;
        return trialSum;
    }

    public void report() {
        System.out.println("After " + trials + " simulations: ");
        System.out.println("Biggest sum: " + max);
        System.out.println("Smallest sum: " + min);
        System.out.println("The average is: " + (double)sum / trials);
    }

    public static void main(String[] args) {
        int trials = Integer.parseInt(args[0]);

        DiceSimulation sim = new DiceSimulation();
        for (int count = 0; count &lt; trials; count++) {
            sim.runTrial();
        }
        sim.report();
    }
}