Just to keep the post upgraded, I have tried: trjconv -pbc nojump -o test.xtc then trjconv -fit rot+trans -f test.xtc -o test1.xtc and then run g_mindist on test1.xtc. The results of -pi is more or less the same that I obtain using vmd program.
Probably it might help other people with the same problem, Regards andrea Yang Ye wrote: > On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote: >> At 08:00 AM 6/12/2007, you wrote: >>> 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 >> >> Hi Andrea, >> >> When you have a multi-chain protein (or a protein + peptide) it can >> happen that when making protein whole (removing pbc) sometimes the two >> chains can be placed in two different adjacent boxes, so... when doing >> the "g_mindist -pi" setup, the closest distance is when they are >> together in the same box at a distance of ~1.7 Angstrom. >> >> Point 1 - This is an artifact, but it doesn't exclude the possibility >> that there are structures seeing their periodic images. As it was >> suggested by Mark Abraham, you should check these structures just to >> be sure. >> >> Point 2 - If someone knows how to trick trjconv -pbc in order to avoid >> doing this... it would be appreciated. > Yes. I got such "separated chain" trajectory with dsDNA as well. I have > a script to move them back manually frame per frame by comparing minimal > distance and real distance. >> >> Miguel >> >> >> ======================================== >> Miguel Machuqueiro >> ITQB-Instituto de Tecnologia Química e Biológica >> Universidade Nova de Lisboa >> Molecular Simulation Group - 6º Floor (Room 601) >> Av. da República, EAN, Apartado 127 >> 2781-901 Oeiras, Portugal >> Tel. : +351 214469618 /Mobile: +351 96 7562285 >> E-mail: machuque at itqb.unl.pt >> _________________________________________ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 >> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users@gromacs.org 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
