[gmx-users] question about periodic boundary conditions
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 20 22:58:30 CEST 2010
rainy908 at yahoo.com wrote:
> Hi Justin,
>
> Thanks for getting back to me. I executed the following command using
> g_mindist:
>
> $gromacs/g_mindist -pi -f n12_random_all.xtc -s n12_random.tpr -n
> index.ndx -od mindist.xvg
>
> ..and got the output (see below). It shows that the minimal distance to
> periodic image is at the most a few nm, but when I look in VMD, it is
> very apparent that there overlap between portions of the molecule. If
> so, wouldn't the minimal distance be negative? I've even executed the
> above command with the -pbc flag, and get the same output.
>
> I'm not sure how to interpret these results. Any additional feedback
> on your end would be greatly appreciated.
>
Without context, I don't know how to interpret your results either. Do you have
a single solute? Or multiple equivalent molecules?
If you have a single solute, I think it's quite likely that your molecule of
interest has seen its periodic image. You shouldn't be concerned with the
largest value you see, you should be concerned with the smallest. Towards the
end of your output, you've got values as low as ~0.55 nm. I'm assuming that
you're using conventional cutoffs of no smaller than 1.0 nm or so, in which case
you've very clearly violated the minimum image convention. This agrees with
your observations using VMD.
-Justin
> Thanks,
> Lili
>
>
>
> # Giant Rising Ordinary Mutants for A Clerical Setup
> #
> @ title "Minimum distance to periodic image"
> @ xaxis label "Time (ps)"
> @ yaxis label "Distance (nm)"
> @TYPE xy
> @ subtitle "and maximum internal distance"
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "min per."
> @ s1 legend "max int."
> @ s2 legend "box1"
> @ s3 legend "box2"
> @ s4 legend "box3"
> 0 4.226 22.198 20.402 8.824 15.015
> 500 3.475 21.944 19.423 8.400 14.296
> 1000 4.266 21.065 19.420 8.397 14.295
> 1500 3.934 21.430 19.421 8.396 14.297
> 2000 3.999 21.850 19.424 8.395 14.301
> 2500 4.031 20.793 19.426 8.394 14.303
> 3000 3.469 21.160 19.425 8.392 14.304
> 3500 3.902 21.372 19.425 8.390 14.305
> 4000 4.321 20.999 19.424 8.388 14.306
> 4500 4.667 19.447 19.428 8.388 14.310
> 5000 4.794 19.991 19.430 8.387 14.312
> 5500 4.909 19.142 19.430 8.384 14.313
> 6000 5.317 19.153 19.432 8.383 14.315
> 6500 5.110 19.223 19.431 8.381 14.315
> 7000 4.864 19.127 19.434 8.380 14.318
> 7500 4.246 18.680 19.438 8.380 14.322
> 8000 4.508 18.937 19.438 8.377 14.322
> 8500 4.441 17.865 19.440 8.376 14.324
> 9000 4.104 19.036 19.438 8.373 14.324
> 9500 4.676 18.528 19.439 8.371 14.325
> 10000 4.313 18.953 19.443 8.371 14.328
> 10500 4.045 18.462 19.441 8.368 14.328
> 11000 5.013 19.162 19.443 8.367 14.330
> 11500 5.131 18.435 19.446 8.366 14.333
> 12000 5.054 17.814 19.447 8.364 14.335
> 12500 4.792 17.266 19.445 8.361 14.334
> 13000 3.684 16.897 19.451 8.361 14.339
> 13500 3.885 16.450 19.451 8.359 14.340
> 14000 4.007 17.088 19.453 8.357 14.342
> 14500 3.846 17.498 19.456 8.356 14.345
>
> <snip>
>
> 172500 0.619 12.210 19.702 7.999 14.791
> 173000 0.668 12.609 19.703 8.000 14.793
> 173500 0.559 12.401 19.702 7.999 14.793
> 174000 0.507 12.638 19.701 8.000 14.794
> 174500 0.518 12.512 19.697 7.998 14.792
> 175000 0.757 12.316 19.701 8.000 14.796
> 175500 0.581 12.105 19.696 7.998 14.793
> 176000 0.810 11.777 19.696 7.999 14.794
> 176500 0.763 11.521 19.694 7.998 14.794
> 177000 0.666 11.886 19.697 7.999 14.797
> 177500 0.760 11.598 19.694 7.999 14.796
> 178000 0.495 11.356 19.689 7.997 14.793
> 178500 0.782 11.741 19.693 7.999 14.797
> 179000 0.509 11.908 19.692 7.999 14.798
> 179500 0.654 12.413 19.690 7.998 14.797
> 180000 0.840 12.171 19.694 8.000 14.801
> 180500 0.631 12.090 19.690 7.999 14.800
> 181000 0.511 12.345 19.692 8.000 14.802
> 181500 0.494 12.205 19.688 7.999 14.801
> 182000 0.579 13.061 19.689 8.000 14.803
> 182500 0.496 13.220 19.687 7.999 14.803
>
> <snip>
>
> 1.02e+06 0.785 13.881 19.555 7.999 14.902
> 1.0205e+06 0.920 13.526 19.552 7.998 14.900
> 1.021e+06 0.764 12.981 19.551 7.998 14.899
> 1.0215e+06 1.000 13.326 19.554 7.999 14.901
> 1.022e+06 0.983 13.016 19.552 7.998 14.899
> 1.0225e+06 0.969 13.209 19.553 7.999 14.900
> 1.023e+06 0.826 13.377 19.555 7.999 14.901
> 1.0235e+06 0.717 12.895 19.555 7.999 14.901
> 1.024e+06 0.868 13.191 19.555 7.999 14.902
> 1.0245e+06 0.868 12.682 19.557 8.000 14.903
> 1.025e+06 0.524 12.980 19.556 8.000 14.903
> 1.0255e+06 0.468 13.197 19.558 8.001 14.904
> 1.026e+06 0.715 13.212 19.554 7.999 14.901
> 1.0265e+06 0.547 12.988 19.556 7.999 14.902
> 1.027e+06 0.777 12.686 19.552 7.998 14.900
> 1.0275e+06 0.798 12.490 19.555 7.999 14.902
> 1.028e+06 0.702 12.716 19.554 7.999 14.901
> 1.0285e+06 0.661 12.851 19.555 7.999 14.902
> 1.029e+06 0.505 12.433 19.553 7.999 14.901
> 1.0295e+06 0.889 12.451 19.557 8.000 14.904
> 1.03e+06 0.769 12.860 19.553 7.998 14.900
> 1.0305e+06 0.558 12.903 19.559 8.001 14.905
> 1.031e+06 0.857 13.268 19.557 8.000 14.904
>
>
> On 20 October 2010 13:22, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> rainy908 at yahoo.com <mailto:rainy908 at yahoo.com> wrote:
>
> Hi,
>
> Is there a way to quantitatively determine, from a trajectory
> file, whether a molecule is interacting with a copy of itself in
> the adjacent box (given that PBC is applied)? Currently, I'm
> using VMD - I've already loaded the *xtc file into the*gro
> structure file and viewed the "periodic images to draw" under
> the Periodic tab of Graphical Representations.
> But I figure there's got to be an analytical way to do this,
> using g_dist or g_mindist? How the molecule is interacting
> (with its adjacent copy) is not the primary interest - I just
> want to know whether interactions among adjacent molecules are
> occurring.
>
>
> >From g_mindist -h:
>
> "With option -pi the minimum distance of a group to its periodic
> image is
> plotted. This is useful for checking if a protein has seen its
> periodic image
> during a simulation. Only one shift in each direction is considered,
> giving a
> total of 26 shifts. It also plots the maximum distance within the
> group and
> the lengths of the three box vectors."
>
> -Justin
>
>
> Does anyone have any ideas?
>
> Thanks,
> Lili
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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