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/ > ------------------------------- > > ******************************************************************** > 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 [EMAIL PROTECTED] o vai sul sito > w w w . 5 x m i l l e . o r g > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ------------------------------- 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 [EMAIL PROTECTED] o vai sul sito w w w . 5 x m i l l e . o r g _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
