Is it possible to obtain %0.05 duty cycle at 1hz in arduino?(a 500us square pulse at 1 sec period) I have a system which requires me to obtain different duty cycles at different frequencies. But using the analogWrite() does not allow me to obtain a value lower than 1/255 duty cycle. I need to obtain lower duty cycle values for 1Hz
Expanding from my comment. This is an attempt to generate that signal with Timer 1. No time to test it now... Edit: tested, works as advertised.

/*
 * Configure Timer 1 to generate a slow, low duty cycle PWM signal.
 * Output pin = digital 9 = PB1 = OC1A.
 */

const float PWM_PERIOD  = 1.0;     // 1 s
const float PULSE_WIDTH = 500e-6;  // 500 us

/*
 * With a 16 MHz clock and this prescaler, the resolution is 16 us and
 * the maximum period is 1.048576 s.
 */
const uint16_t TIMER_PRESCALER = 256;
const float F_TIMER = F_CPU / TIMER_PRESCALER;

void setup()
{
    // Configure Timer 1.
    DDRB  |= _BV(PB1);    // set PB1 = OC1A as output
    ICR1   = round(PWM_PERIOD * F_TIMER) - 1;
    OCR1A  = round(PULSE_WIDTH * F_TIMER) - 1;
    TCCR1A = _BV(COM1A1)  // non-inverting PWM on OC1A
           | _BV(WGM11);  // fast PWM mode, TOP = ICR1
    TCCR1B = _BV(WGM12)   // ditto
           | _BV(WGM13)   // ditto
           | _BV(CS12);   // clock at F_CPU/256 = 62.5 kHz
}

void loop() {}