On Mon, 2006-12-18 at 14:13 +0100, Florian Haberl wrote: > hi, > > On Monday 18 December 2006 12:34, OZGE ENGIN wrote: > > Hi, > > > > I have a problem with g_hbond. I want to investigate the H bonds formed not > > only within the protein but also between water molecules and the protein.In > > this respect, I select the group 0 --> 'system' option for both > > selections, an error message like the following one appears: > > > > Segmentation fault > > > > How can I fix this problem? > > Please describe your system more: > how many atoms > how many water molecules > ... > > Does g_hbond run with your test system (20 aa some water molecules) > > I think it is a memory problem, if you take too much atoms into account > g_hbond can consume a little bit more memory (depends also on your options) >
Yes, I think so too. Could you split your analysis into different parts? Someting like: (I) protein-protein, (II) solvent-pprotein and (III) solvent-solvent h-bonds. That would reduce the required memory. /Erik > > > > > Thanks in advance > > > > Ozge > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > 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 > > > Greetings, > > Florian > -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
