The basic format of your code should be 1> read in input data 2> determine initial coordinates (coord[i].x,coord[i].y,coord[i].z) 3> determine forces at coordinates (force[i].x,force[i].y,force[i].z) 4> determine potential at coordinates (PE) 5> initialize velocity to zero (vel[i].x,vel[i].y,vel[i].z) 6> Loop over timesteps 7> determine KE 8> print PE, KE, PE+KE 9> update coordinates (coord[i].x=coord[i].x+..., and for y and z) 10> determine force at new coordinates (newf[i].x,newf[i].y,newf[i].z) 11> determine potential at new coordinates (PE) 12> update velocity (vel[i].x +=(force[i].x+newf[i].x) etc for y/z 13> force[i].x=newf[i].x 14> repeat 6 ===================== OUTPUT 0 ===================== Basic MD Program: md_unopt Dimension of Cube 2.000000 Total atoms 27 Time step 0.001000 Number of steps 10 TIME Total Energy PE KE ------------------------------------------------------------------- 0.000000 -7.577011e+01 -7.577011e+01 0.000000e+00 0.001000 -7.577011e+01 -7.577026e+01 1.504815e-04 0.002000 -7.577011e+01 -7.577071e+01 6.018923e-04 0.003000 -7.577011e+01 -7.577147e+01 1.354131e-03 0.004000 -7.577011e+01 -7.577252e+01 2.407030e-03 0.005000 -7.577011e+01 -7.577387e+01 3.760354e-03 0.006000 -7.577011e+01 -7.577552e+01 5.413798e-03 0.007000 -7.577011e+01 -7.577748e+01 7.366993e-03 0.008000 -7.577011e+01 -7.577973e+01 9.619501e-03 0.009000 -7.577011e+01 -7.578228e+01 1.217082e-02 Thats all folks ===================== OUTPUT 1 ===================== Basic MD Program: md_unopt Dimension of Cube 2.000000 Total atoms 27 Time step 0.100000 Number of steps 10 TIME Total Energy PE KE ------------------------------------------------------------------- 0.000000 -7.577011e+01 -7.577011e+01 0.000000e+00 0.100000 -7.598907e+01 -7.704081e+01 1.051739e+00 0.200000 -7.626497e+01 -7.740702e+01 1.142043e+00 0.300000 -7.554373e+01 -7.564457e+01 1.008397e-01 0.400000 -7.617098e+01 -7.768747e+01 1.516487e+00 0.500000 -7.579469e+01 -7.638111e+01 5.864200e-01 0.600000 -7.572068e+01 -7.594542e+01 2.247414e-01 0.700000 -7.608452e+01 -7.748455e+01 1.400029e+00 0.800000 -7.577690e+01 -7.640108e+01 6.241828e-01 0.900000 -7.587327e+01 -7.653950e+01 6.662278e-01 Thats all folks ===================== OUTPUT 3 ===================== Basic MD Program: md_unopt Dimension of Cube 3.000000 Total atoms 27 Time step 0.100000 Number of steps 10 TIME Total Energy PE KE ------------------------------------------------------------------- 0.000000 -1.107111e+01 -1.107111e+01 0.000000e+00 0.100000 -1.106964e+01 -1.124086e+01 1.712215e-01 0.200000 -1.106469e+01 -1.177428e+01 7.095849e-01 0.300000 -1.105446e+01 -1.275192e+01 1.697461e+00 0.400000 -1.103458e+01 -1.433938e+01 3.304794e+00 0.500000 -1.099488e+01 -1.685570e+01 5.860813e+00 0.600000 -1.091000e+01 -2.093443e+01 1.002444e+01 0.700000 -1.071413e+01 -2.792570e+01 1.721157e+01 0.800000 -1.028891e+01 -4.090534e+01 3.061643e+01 0.900000 -1.137071e+01 -6.518048e+01 5.380978e+01 Thats all folks =============================================================== OUTPUT 4 WITH COORDINATES, FORCE and VELOCITY =============================================================== Basic MD Program: md_unopt Dimension of Cube 1.500000 Total atoms 27 Time step 0.010000 Number of steps 2 TIME Total Energy PE KE ------------------------------------------------------------------- No xyz Coord Force Veloc 0 x 0.00000 -409.08769 0.00000 y 0.00000 -409.08769 0.00000 z 0.00000 -409.08769 0.00000 1 x 0.00000 -406.32945 0.00000 y 0.00000 -406.32945 0.00000 z 0.75000 0.00000 0.00000 2 x 0.00000 -409.08769 0.00000 y 0.00000 -409.08769 0.00000 z 1.50000 409.08769 0.00000 3 x 0.00000 -406.32945 0.00000 y 0.75000 0.00000 0.00000 z 0.00000 -406.32945 0.00000 4 x 0.00000 -402.72446 0.00000 y 0.75000 -0.00000 0.00000 z 0.75000 0.00000 0.00000 5 x 0.00000 -406.32945 0.00000 y 0.75000 -0.00000 0.00000 z 1.50000 406.32945 0.00000 6 x 0.00000 -409.08769 0.00000 y 1.50000 409.08769 0.00000 z 0.00000 -409.08769 0.00000 7 x 0.00000 -406.32945 0.00000 y 1.50000 406.32945 0.00000 z 0.75000 0.00000 0.00000 8 x 0.00000 -409.08769 0.00000 y 1.50000 409.08769 0.00000 z 1.50000 409.08769 0.00000 9 x 0.75000 0.00000 0.00000 y 0.00000 -406.32945 0.00000 z 0.00000 -406.32945 0.00000 10 x 0.75000 0.00000 0.00000 y 0.00000 -402.72446 0.00000 z 0.75000 0.00000 0.00000 11 x 0.75000 -0.00000 0.00000 y 0.00000 -406.32945 0.00000 z 1.50000 406.32945 0.00000 12 x 0.75000 0.00000 0.00000 y 0.75000 0.00000 0.00000 z 0.00000 -402.72446 0.00000 13 x 0.75000 -0.00000 0.00000 y 0.75000 -0.00000 0.00000 z 0.75000 0.00000 0.00000 14 x 0.75000 -0.00000 0.00000 y 0.75000 -0.00000 0.00000 z 1.50000 402.72446 0.00000 15 x 0.75000 0.00000 0.00000 y 1.50000 406.32945 0.00000 z 0.00000 -406.32945 0.00000 16 x 0.75000 -0.00000 0.00000 y 1.50000 402.72446 0.00000 z 0.75000 0.00000 0.00000 17 x 0.75000 -0.00000 0.00000 y 1.50000 406.32945 0.00000 z 1.50000 406.32945 0.00000 18 x 1.50000 409.08769 0.00000 y 0.00000 -409.08769 0.00000 z 0.00000 -409.08769 0.00000 19 x 1.50000 406.32945 0.00000 y 0.00000 -406.32945 0.00000 z 0.75000 0.00000 0.00000 20 x 1.50000 409.08769 0.00000 y 0.00000 -409.08769 0.00000 z 1.50000 409.08769 0.00000 21 x 1.50000 406.32945 0.00000 y 0.75000 0.00000 0.00000 z 0.00000 -406.32945 0.00000 22 x 1.50000 402.72446 0.00000 y 0.75000 -0.00000 0.00000 z 0.75000 0.00000 0.00000 23 x 1.50000 406.32945 0.00000 y 0.75000 -0.00000 0.00000 z 1.50000 406.32945 0.00000 24 x 1.50000 409.08769 0.00000 y 1.50000 409.08769 0.00000 z 0.00000 -409.08769 0.00000 25 x 1.50000 406.32945 0.00000 y 1.50000 406.32945 0.00000 z 0.75000 0.00000 0.00000 26 x 1.50000 409.08769 0.00000 y 1.50000 409.08769 0.00000 z 1.50000 409.08769 0.00000 0.000000 1.006262e+03 1.006262e+03 0.000000e+00 No xyz Coord Force Veloc 0 x -0.02045 -275.56345 -3.42326 y -0.02045 -275.56345 -3.42326 z -0.02045 -275.56345 -3.42326 1 x -0.02032 -273.36141 -3.39845 y -0.02032 -273.36141 -3.39845 z 0.75000 0.00000 0.00000 2 x -0.02045 -275.56345 -3.42326 y -0.02045 -275.56345 -3.42326 z 1.52045 275.56345 3.42326 3 x -0.02032 -273.36141 -3.39845 y 0.75000 -0.00000 0.00000 z -0.02032 -273.36141 -3.39845 4 x -0.02014 -270.56945 -3.36647 y 0.75000 -0.00000 -0.00000 z 0.75000 -0.00000 -0.00000 5 x -0.02032 -273.36141 -3.39845 y 0.75000 0.00000 -0.00000 z 1.52032 273.36141 3.39845 6 x -0.02045 -275.56345 -3.42326 y 1.52045 275.56345 3.42326 z -0.02045 -275.56345 -3.42326 7 x -0.02032 -273.36141 -3.39845 y 1.52032 273.36141 3.39845 z 0.75000 0.00000 0.00000 8 x -0.02045 -275.56345 -3.42326 y 1.52045 275.56345 3.42326 z 1.52045 275.56345 3.42326 9 x 0.75000 -0.00000 -0.00000 y -0.02032 -273.36141 -3.39845 z -0.02032 -273.36141 -3.39845 10 x 0.75000 -0.00000 -0.00000 y -0.02014 -270.56945 -3.36647 z 0.75000 -0.00000 -0.00000 11 x 0.75000 -0.00000 -0.00000 y -0.02032 -273.36141 -3.39845 z 1.52032 273.36141 3.39845 12 x 0.75000 -0.00000 -0.00000 y 0.75000 -0.00000 -0.00000 z -0.02014 -270.56945 -3.36647 13 x 0.75000 -0.00000 -0.00000 y 0.75000 -0.00000 -0.00000 z 0.75000 -0.00000 -0.00000 14 x 0.75000 -0.00000 -0.00000 y 0.75000 0.00000 -0.00000 z 1.52014 270.56945 3.36647 15 x 0.75000 -0.00000 0.00000 y 1.52032 273.36141 3.39845 z -0.02032 -273.36141 -3.39845 16 x 0.75000 0.00000 0.00000 y 1.52014 270.56945 3.36647 z 0.75000 -0.00000 -0.00000 17 x 0.75000 0.00000 0.00000 y 1.52032 273.36141 3.39845 z 1.52032 273.36141 3.39845 18 x 1.52045 275.56345 3.42326 y -0.02045 -275.56345 -3.42326 z -0.02045 -275.56345 -3.42326 19 x 1.52032 273.36141 3.39845 y -0.02032 -273.36141 -3.39845 z 0.75000 0.00000 0.00000 20 x 1.52045 275.56345 3.42326 y -0.02045 -275.56345 -3.42326 z 1.52045 275.56345 3.42326 21 x 1.52032 273.36141 3.39845 y 0.75000 -0.00000 0.00000 z -0.02032 -273.36141 -3.39845 22 x 1.52014 270.56945 3.36647 y 0.75000 -0.00000 -0.00000 z 0.75000 -0.00000 -0.00000 23 x 1.52032 273.36141 3.39845 y 0.75000 0.00000 -0.00000 z 1.52032 273.36141 3.39845 24 x 1.52045 275.56345 3.42326 y 1.52045 275.56345 3.42326 z -0.02045 -275.56345 -3.42326 25 x 1.52032 273.36141 3.39845 y 1.52032 273.36141 3.39845 z 0.75000 0.00000 0.00000 26 x 1.52045 275.56345 3.42326 y 1.52045 275.56345 3.42326 z 1.52045 275.56345 3.42326 0.010000 9.498870e+02 6.366695e+02 3.132174e+02 Thats all folks