Hi, I use the 3.3.1 version of gromacs.
My system consists of a capped alanine residue embedded in a box of 500 water molecules. When I select the group 1 option ( only capped alanine residue) there is no error; however, an error occurs due to selection of the whole system (group 0 option). I want to investigate the hydrogen bonds not only formed within the protein but also between the protein molecule (capped alanine residue) and water molecules. Moreover, i could not understand the memory problem. Could you explain it in detail,please? Thanks in advance Ozge -----Original Message----- From: Erik Marklund <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Date: Mon, 18 Dec 2006 13:48:18 +0100 Subject: Re: [gmx-users] g_hbond On Mon, 2006-12-18 at 13:34 +0200, 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? That's hard to say. Which version are you running? > > 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 /Erik -- 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 _______________________________________________ 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
