[gmx-users] Periodic Boundary Conditions g_mindist -pi

[ifat shub]

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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