On Mon, 2006-12-18 at 22:57 +0200, OZGE ENGIN wrote: > 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?
One thing is that the existence matrix for all the hydrogen bonds is HUGE if you choose large groups for the analysis. Let's say you have 5000 water molecules and a protein having 100 donors/acceptors, adding up to a total of 5100 donors/acceptors, and that the number of frames in your trajectory is 10000. That gives you a maximum size of 5100x5100x10000 = 260100000000 elements. That's a lot of memory. However, the matrix will never reach that size for two reasons: 1) some potential hydrogen bonds will never form, e.g. because they are too far apart. 2) not all frames of the existence function is stored in the matrix, only the ones from the first instance of a particular hydrogen bond to its last occurrence. Nevertheless, the calculations illustrate a potential memory problem arising from having a system too big. This is also why i suggested you should split the analysis into parts: solvent-solute ... /Erik > > 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
