[gmx-users] Re: grompp for minimization: note & warning
Mark Abraham
mark.j.abraham at gmail.com
Fri Sep 20 13:59:03 CEST 2013
The UNIX tool diff is your friend for comparing files.
On Fri, Sep 20, 2013 at 1:53 PM, shahab shariati
<shahab.shariati at gmail.com> wrote:
> 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.
> --
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