[gmx-users] question about periodic boundary conditions
rainy908 at yahoo.com
rainy908 at yahoo.com
Wed Oct 20 22:51:09 CEST 2010
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.
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> wrote:
>
>
> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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