[gmx-users] question about periodic boundary conditions
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 20 23:47:53 CEST 2010
rainy908 at yahoo.com wrote:
>
> Justin,
>
> I have a single solute. But I understand what you're saying about the
> cutoff. My long-range cutoff is set to 1.2 nm (from MARTINI force
> field), so therefore, the snapshots corresponding to a minimum periodic
> distance of < 1.2 nm would agree with the overlap witnessed in VMD?
>
Indeed. You've violated the minimum image convention.
-Justin
> Thanks again,
> Lili
>
> On 20 October 2010 13:58, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> rainy908 at yahoo.com <mailto: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> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
>
> rainy908 at yahoo.com <mailto:rainy908 at yahoo.com>
> <mailto: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> <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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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--
========================================
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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