[gmx-users] problem with g_dist (probably solved)

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Nov 2 21:51:05 CET 2008

Hi Thomas,

To have PBC or not in a run has nothing to do with analysis. Analysis
tools don't have a clue of what you put into the .mdp files. Any of
tha analysis tools will assume that the box specified in the file
involves PBC. Don't know from the top of my head, but I think where
possibly necessary, tools offer an option -nopbc. If g_dist doesn't
have that, it probably should :) (and in that case you might want to
submit it to bugzilla).



On Sun, Nov 2, 2008 at 3:14 PM, Thomas Schlesier <schlesi at uni-mainz.de> wrote:
> Hi all,
> i had problems with g_dist. My system consists of 15 molecules urea with
> a short alkane linker. With constraints and restraintss (distance,
> angles and dihedrals) made it that the molecules are in one line (the
> last methyl-group of the alkan linker).
> Here a little picture:
> ________  ...
> |      |       |    ...
> X    X     X   ...
> | is the alkan linker; X is the urea-group and _____  is the line which
> conacts the methyl-groups.
> The distance between each molecule is 2nm, so (with 15 molecules) the
> distance between the first and the last molecule should be 28nm. The
> size of the simulation box was 40 10 10 (all nm), with no pbc (periodic
> boundary conditions) (the 'line' was along the x-axis).
> When i determined the distance between the first and the last molecule
> with g_dist, the program gave some errors:  "There were 1 inconsistent
> shifts. Check your topology" , but the program ended normally. The
> calculeted distance was around 12nm (versus the 28nm which is the
> correct value; i calculated it from the .gro file).
> So my idea was the g_dist uses pbc to calculate the distance (even if
> the simulation had no pbc). The distance between the first and the last
> methyl-group (in the two nearest boxes) should be around 40nm (box size)
> -28nm (distance in one box) = 12 nm (distaance over two boxes).
> Is this idea right?!?
> In another simulation i increased the box size to 60 60 60 (nm). Here
> g_dist had no troubles. I get no error messages ("There were 1
> inconsistent shifts. Check your topology") and the distance is right.
> The other question is: What does the error message mean?
> Thanks for your help.
> Thomas
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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