[gmx-users] g_mindist -pi option

[andrea spitaleri]

Hi there,
I have a complex protein-peptide in a box 6.5 6.5 6.5 with a starting periodic image of 3.0 nm,
using PME and rlist=rvdw=rcoulomb=0.9.
Now, I use to check the pi dist during my simulation in order to make sure that the box is larger
enough. After 6ns I get this result:
        0        3.018  4.711  6.555  6.555  6.555
        30       2.791  4.514  6.557  6.557  6.557
        60       2.721  4.270  6.555  6.555  6.555
        90       2.762  4.378  6.554  6.554  6.554
....................
	4620     3.017  4.042  6.558  6.558  6.558
        4650     0.173  9.080  6.548  6.548  6.548
        4680     2.700  3.949  6.561  6.561  6.561
        4710     2.881  4.113  6.560  6.560  6.560
...................
        6000     2.939  4.049  6.556  6.556  6.556

So it seems that there is a "spike" around 4650 ps of a very low distance (quite worrying me).
Any hints? is it true this value or is it pbc artefact?
Thanks in advance

Regards,

and

ps. gmx3-3-1 compiled on suse-10.2 gcc-v 4.1.2

 --
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------

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