[gmx-users] Periodic Boundary Conditions g_mindist -pi

[Tsjerk Wassenaar]

Hi Ifat,

I guess this is a jump over the periodic boundaries. You should remove
jumps from the trajectory (-pbc nojump) before running g_mindist -pi.

Cheers,

Tsjerk

On Wed, Feb 16, 2011 at 10:19 AM, ifat shub <shubifat at gmail.com> wrote:
> Hi,
>
>
>
> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
> if the complex is seeing its next periodic image, so I used the g_mindist
> command with the -pi option. My command line was:
>
> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>
> The output (see below) was stable until ~344ps when there is a  jump in the
> max internal distance (third column) from ~6nm to ~22nm. After the jump the
> numbers are reduced back to ~6nm and remained stable until the run is
> completed at 1ns.
>
> Does anyone know how to explain this jump? Is this a real problem or just a
> visualization artifact? Is there a way to avoid such jumps?
>
>
>
> Here is the mdp file I used:
>
> ------run.mdp------
>
> integrator      = md
>
> nsteps          = 1000000
>
> dt              = 0.001
>
> coulombtype     = pme
>
> vdw-type        = cut-off
>
> tcoupl          = Berendsen
>
> tc-grps         = protein non-protein
>
> tau-t           = 0.1 0.1
>
> ref-t           = 310 310
>
> nstxout         = 100
>
> nstvout         = 0
>
> nstxtcout       = 100
>
> nstenergy           = 100
>
> comm_mode     = Linear ; Angular
>
> comm_grps        = Protein
>
> xtc_grps               = Protein
>
> energygrps         = Protein
>
> ------------------
>
>
>
> Thanks,
>
> Ifat
>
>
>
> The output:
>
> 343.7   10.813 5.924   16.445 16.445 16.445
>
> 343.8   10.809 5.949   16.445 16.445 16.445
>
> 343.9   10.804 5.959   16.445 16.445 16.445
>
> 344      10.808 5.974   16.445 16.445 16.445
>
> 344.1   0.18     21.982 16.445 16.445 16.445
>
> 344.2   10.778 5.977   16.445 16.445 16.445
>
> 344.3   10.768 5.996   16.445 16.445 16.445
>
> 344.4   10.764 6.016   16.445 16.445 16.445
>
> 344.5   10.722 6.029   16.445 16.445 16.445
>
> 344.6   10.774 6.01     16.445 16.445 16.445
>
> 344.7   0.174   21.984 16.445 16.445 16.445
>
> 344.8   0.176   21.98   16.445 16.445 16.445
>
> 344.9   0.17     22.002 16.445 16.445 16.445
>
> 345      0.173   21.981 16.445 16.445 16.445
>
> 345.1   0.191   21.954 16.445 16.445 16.445
>
> 345.2   0.183   21.958 16.445 16.445 16.445
>
> 345.3   0.181   22.012 16.445 16.445 16.445
>
> 345.4   0.17     22.054 16.445 16.445 16.445
>
> 345.5   0.168   22.054 16.445 16.445 16.445
>
> 345.6   0.189   22.039 16.445 16.445 16.445
>
> 345.7   0.171   22.007 16.445 16.445 16.445
>
> 345.8   0.186   22.031 16.445 16.445 16.445
>
> 345.9   0.171   22.077 16.445 16.445 16.445
>
> 346      0.187   21.99   16.445 16.445 16.445
>
> 346.1   0.173   21.984 16.445 16.445 16.445
>
> 346.2   0.181   22.02   16.445 16.445 16.445
>
> 346.3   10.82   5.984   16.445 16.445 16.445
>
> 346.4   10.81   6.002   16.445 16.445 16.445
>
> 346.5   10.819 6.008   16.445 16.445 16.445
>
> 346.6   10.813 5.996   16.445 16.445 16.445
>
> 346.7   10.781 6.006   16.445 16.445 16.445
>
> 346.8   10.793 6.026   16.445 16.445 16.445
>
> 346.9   10.745 5.985   16.445 16.445 16.445
>
> 347      10.762 5.999   16.445 16.445 16.445
>
> 347.1   10.781 5.984   16.445 16.445 16.445
>
> 347.2   10.784 6.002   16.445 16.445 16.445
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands