Hi again,
since I did not get answer I double checked my trr file. In case I calculate the minimum distance of
the periodic image for each component of my complex, I get reasonable value of it (3.0 and 2.9 nm),
whereas if I consider the whole system (protein) I get this strange result of 0.17 nm.
Any clue?
thanks again
Regards
andrea
andrea spitaleri wrote:
> 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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--
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------
********************************************************************
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria")
il codice fiscale della
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai sul sito
w w w . 5 x m i l l e . o r g