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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