[gmx-users] Re: grompp for minimization: note & warning
shahab shariati
shahab.shariati at gmail.com
Fri Sep 20 13:53:34 CEST 2013
Dear Tsjerk
Thanks for your reply
Before correcting the gro file, I knew that gro file is fixed format.
I did this correction very carefully.
Part of the gro file before and after correction is as follows:
---------------------------------------------
before:
---------------------------------------------
14DOPC N4 755 0.260 1.726 6.354
14DOPC C5 756 0.263 1.741 6.204
14DOPC C1 757 0.136 1.777 6.423
14DOPC C2 758 0.279 1.580 6.384
14DOPC C3 759 0.383 1.799 6.403
14DOPC C6 760 0.386 1.685 6.132
14DOPC P8 761 0.628 1.683 6.064
14DOPC OM9 762 0.640 1.548 6.123
14DOPC OM10 763 0.747 1.771 6.072
14DOPC OS7 764 0.511 1.755 6.145
14DOPC OS11 765 0.576 1.681 5.913
14DOPC C12 766 0.591 1.806 5.845
14DOPC C13 767 0.470 1.901 5.846
14DOPC OS14 768 0.364 1.830 5.782
14DOPC C15 769 0.247 1.869 5.833
14DOPC O16 770 0.238 1.946 5.927
14DOPC C17 771 0.123 1.815 5.762
14DOPC C34 772 0.490 2.037 5.777
14DOPC OS35 773 0.541 2.029 5.644
14DOPC C36 774 0.591 2.142 5.593
14DOPC O37 775 0.595 2.252 5.646
14DOPC C38 776 0.674 2.092 5.476
14DOPC C18 777 -0.004 1.897 5.786
14DOPC C19 778 -0.138 1.837 5.744
14DOPC C20 779 -0.147 1.817 5.593
14DOPC C21 780 -0.196 1.678 5.552
14DOPC C22 781 -0.181 1.637 5.406
14DOPC C23 782 -0.252 1.722 5.301
14DOPC C24 783 -0.241 1.664 5.163
14DOPC C25 784 -0.267 1.738 5.054
14DOPC C26 785 -0.312 1.881 5.044
14DOPC C27 786 -0.368 1.918 4.907
14DOPC C28 787 -0.266 1.941 4.795
14DOPC C29 788 -0.324 2.015 4.674
14DOPC C30 789 -0.377 1.920 4.567
14DOPC C31 790 -0.377 1.984 4.428
14DOPC C32 791 -0.439 1.894 4.321
14DOPC C33 792 -0.358 1.890 4.191
14DOPC C39 793 0.818 2.145 5.475
14DOPC C40 794 0.906 2.056 5.387
14DOPC C41 795 1.042 2.123 5.364
14DOPC C42 796 1.160 2.029 5.339
14DOPC C43 797 1.136 1.965 5.202
14DOPC C44 798 1.261 1.897 5.146
14DOPC C45 799 1.314 1.786 5.232
14DOPC C46 800 1.319 1.658 5.194
14DOPC C47 801 1.274 1.602 5.062
14DOPC C48 802 1.316 1.457 5.038
14DOPC C49 803 1.266 1.407 4.902
14DOPC C50 804 1.338 1.469 4.782
14DOPC C51 805 1.307 1.406 4.646
14DOPC C52 806 1.160 1.394 4.607
14DOPC C53 807 1.119 1.442 4.468
14DOPC C54 808 0.980 1.407 4.414
---------------------------------------------
after:
---------------------------------------------
14DOPC C1 755 0.136 1.777 6.423
14DOPC C2 756 0.279 1.580 6.384
14DOPC C3 757 0.383 1.799 6.403
14DOPC N4 758 0.260 1.726 6.354
14DOPC C5 759 0.263 1.741 6.204
14DOPC C6 760 0.386 1.685 6.132
14DOPC OS7 761 0.511 1.755 6.145
14DOPC P8 762 0.628 1.683 6.064
14DOPC OM9 763 0.640 1.548 6.123
14DOPC OM10 764 0.747 1.771 6.072
14DOPC OS11 765 0.576 1.681 5.913
14DOPC C12 766 0.591 1.806 5.845
14DOPC C13 767 0.470 1.901 5.846
14DOPC OS14 768 0.364 1.830 5.782
14DOPC C15 769 0.247 1.869 5.833
14DOPC O16 770 0.238 1.946 5.927
14DOPC C17 771 0.123 1.815 5.762
14DOPC C18 772 -0.004 1.897 5.786
14DOPC C19 773 -0.138 1.837 5.744
14DOPC C20 774 -0.147 1.817 5.593
14DOPC C21 775 -0.196 1.678 5.552
14DOPC C22 776 -0.181 1.637 5.406
14DOPC C23 777 -0.252 1.722 5.301
14DOPC C24 778 -0.241 1.664 5.163
14DOPC C25 779 -0.267 1.738 5.054
14DOPC C26 780 -0.312 1.881 5.044
14DOPC C27 781 -0.368 1.918 4.907
14DOPC C28 782 -0.266 1.941 4.795
14DOPC C29 783 -0.324 2.015 4.674
14DOPC C30 784 -0.377 1.920 4.567
14DOPC C31 785 -0.377 1.984 4.428
14DOPC C32 786 -0.439 1.894 4.321
14DOPC C33 787 -0.358 1.890 4.191
14DOPC C34 788 0.490 2.037 5.777
14DOPC OS35 789 0.541 2.029 5.644
14DOPC C36 790 0.591 2.142 5.593
14DOPC O37 791 0.595 2.252 5.646
14DOPC C38 792 0.674 2.092 5.476
14DOPC C39 793 0.818 2.145 5.475
14DOPC C40 794 0.906 2.056 5.387
14DOPC C41 795 1.042 2.123 5.364
14DOPC C42 796 1.160 2.029 5.339
14DOPC C43 797 1.136 1.965 5.202
14DOPC C44 798 1.261 1.897 5.146
14DOPC C45 799 1.314 1.786 5.232
14DOPC C46 800 1.319 1.658 5.194
14DOPC C47 801 1.274 1.602 5.062
14DOPC C48 802 1.316 1.457 5.038
14DOPC C49 803 1.266 1.407 4.902
14DOPC C50 804 1.338 1.469 4.782
14DOPC C51 805 1.307 1.406 4.646
14DOPC C52 806 1.160 1.394 4.607
14DOPC C53 807 1.119 1.442 4.468
14DOPC C54 808 0.980 1.407 4.414
---------------------------------------------
Is there problem in my gro file (after correction)?
I checked manual, my correction is true.
I really do not know how to fix it?
Any help will highly appreciated.
More information about the gromacs.org_gmx-users
mailing list