[gmx-users] g_mindist -pi option

andrea spitaleri spitaleri.andrea at hsr.it
Tue Jun 12 09:00:37 CEST 2007


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



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