Box dimensions will change during NPT simulations. If you wish to keep
static box sizes, you have to use NVT (ntb=1, ntp=0).
However, it seems like your box dimensions are changing a bit *too* much.
Visualizing your trajectory may help show what's going on (as your box is
nearly doubling in size).
Perhaps you're running too hot (and therefore boiling the water).
Good luck,
Jason
On Sat, Mar 19, 2011 at 2:38 PM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> Dear Amber experts,
>
> I need to do some analysis on trajectory files. Principally, I want to
> generate PDB files out from a trajectory file and do some analysis on them
> and later combine back the PDB files to become a single trajectory file as
> before.
>
> For testing the above idea, I have tried with only two frames ( each frame
> for each PDB file) from a trajectory file.
>
> As a first step I have tried to generate two PDB files from a single
> trajectory (mdcrd) file which contain thousands of frames, using PTRAJ (from
> AmberTools-1.4).
>
> As the second step I tried to combine both the PDB files (which have been
> generated earlier) to get a single trajectory (mdcrd) file.
>
> The issue that I would like to inquire here is about the dimensions of the
> BOXES.
> It looks like the BOX dimension at the first step is not CONSISTENT as in
> the second step.
> This might give some problems if I want to use this dimension values for
> further calculation.
>
> Here I have shown below the box dimensions ( the row with only three digits
> )as in the first and second steps respectively.
>
> FIRST STEP ( box dimension before generating PDB files)
>
> 20.991 0.310 86.157 20.496 50.591 8.247 40.965 51.204 8.371
> 40.240
> 51.148 8.199 41.743 38.733 1.877 41.000 39.200 1.538 40.236
> 39.207
> 1.516 41.749 54.260 0.108 41.176 54.536 -0.626 40.627 53.818
> -0.303
> 41.920 42.179 3.556 3.251 41.623 3.530 2.472 42.558 2.678
> 3.304 frame 1
> 44.723 1.496 5.937 44.339 1.355 6.803 44.866 0.614 5.593
> 52.401
> 86.323 2.974 52.385 85.816 3.785 51.879 85.808 2.359
> 56.907 87.404 48.231
> 4.792 5.052 8.317 5.279 4.463 8.898 5.663 5.341 7.220
> 6.267
> 4.438 7.137 6.477 6.566 7.627 5.857 7.407 7.936 7.301
> 6.170
> 8.741 7.647 7.020 9.023 7.315 7.107 6.475 8.171 6.435
> 6.413 frame 2
> 7.823 8.416 6.704 8.208 8.473 7.582 6.560 7.126 5.141
> 5.816
> 7.898 5.335 7.490 7.437 3.932 8.253 6.664 4.029 6.784
> 7.259
> 2.626 5.993 7.803 2.594 7.947 8.415 4.089 5.866 5.845
> 4.942
> 4.920 5.325 5.896 4.617 4.299 5.686 3.680 6.130 5.934
> 2.888
>
> In the SECOND step ( combining two PDB files to become single trajectory
> file)
>
> 20.991 0.310 86.157 20.496 50.591 8.247 40.965 51.204 8.371
> 40.240
> 51.148 8.199 41.743 38.733 1.877 41.000 39.200 1.538 40.236
> 39.207
> 1.516 41.749 54.260 0.108 41.176 54.536 -0.626 40.627 53.818
> -0.303 frame 1
> 41.920 42.179 3.556 3.251 41.623 3.530 2.472 42.558 2.678
> 3.304
> 44.723 1.496 5.937 44.339 1.355 6.803 44.866 0.614 5.593
> 52.401
> 86.323 2.974 52.385 85.816 3.785 51.879 85.808 2.359
> 104.140 159.533 88.303
> 4.792 5.052 8.317 5.279 4.463 8.898 5.663 5.341 7.220
> 6.267
> 4.438 7.137 6.477 6.566 7.627 5.857 7.407 7.936 7.301
> 6.170
> 8.741 7.647 7.020 9.023 7.315 7.107 6.475 8.171 6.435
> 6.413 frame 2
> 7.823 8.416 6.704 8.208 8.473 7.582 6.560 7.126 5.141
> 5.816
> 7.898 5.335 7.490 7.437 3.932 8.253 6.664 4.029 6.784
> 7.259
> 2.626 5.993 7.803 2.594 7.947 8.415 4.089 5.866 5.845
> 4.942
> 4.920 5.325 5.896 4.617 4.299 5.686 3.680 6.130 5.934
> 2.888
>
>
> I am quite curious how to overcome this issue. Is there any technical part
> I need to do the get rid of this differences in the BOX dimensions?
>
> Many thanks in advance.
>
> Regards
>
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
>
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Mar 19 2011 - 17:00:03 PDT
