AMBER Archive (2002)

Subject: Format in a trajectory files is suddenly changed

From: Masaki Tomimoto (masaki_at_stromix.com)
Date: Mon Jul 22 2002 - 11:54:44 CDT

Hi All,

   Does anybody experience the following mystery? I am wondering if the problem was caused by amber7 or by our computer problem.

   I did the same MD calculation (the same input file) twice. Output files were idential except timestamp. Both jobs were succesfully done according to the output files. All coordinates in their restart files generated last were identical. However, in some part of trajectories were different. To matter worse, output format were different, neither.

   A trajectory file contains 670751 lines, however, another does 670257 lines. The former keeps the same output format in it, however, the latter does not like this (The first number in each line indicates the number of lines)

 99317 38.628 22.894 20.827 39.915 23.693 21.480 34.111 24.306 20.416 34.003
 99318 22.926 21.956 33.122 22.483 22.857 33.247 22.674 21.227 31.870 23.373
 99319 20.393 31.802 21.257 20.644 31.889 20.542 21.447 32.082 21.046 20.194
 99320 3 10.6573656 28.0492721 29.7477705
 99321 10.5407093 27.0599108 29.9611127 9.9547494 28.5748845 28.5746347
 99322 10.6858746 29.0937870 27.9528083 9.2860473 27.4510742 27.7490923
 99323 8.7419558 27.8969054 26.9149961 10.3368210 26.4860027 27.1922868
........
  99430 18.4377320 16.4129857 8.7980744 17.6759757 19.7840522 9.0039694
 99431 17.9849284 20.6669698 8.4390979 16.5960228 19.6619848 8.9070193
 99432 17.9299814 19.9249409 10.0539558 20.5793602 10.254 29.270
 99433 4.642 21.040 29.827 6.695 19.977 29.784 7.353 19.409 29.259 7.244
 99434 20.745 30.900 6.474 20.825 31.668 8.463 20.059 31.521 8.248 19.004
 99435 31.679 9.319 20.157 30.855 8.775 20.654 32.768 9.731 20.585 32.908
  
  As you can see above, output format was suddenly changed and then suddenly recovered. All data above 99319 line and below 99433 line were identical with both trajectories.

  I strongly hope someone gives me a clue to solve the mystery.

Thanks,

  Masaki Tomimoto, Ph.D.
  Sr. Scientist
  Computational chemistry department
  Structural GenomiX Inc.