[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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