HI Justin, I just use the mdrun command and then get such error. Before that, I did not get other messages just go on well expect when I use the mdrun.
Also, when I did not use the position_restraints , it will run smoothly. As long as I add this even though the position_restraints includes only one atom, it will show the error. Yang ________________________________________ From: [email protected] [[email protected]] On Behalf Of Justin A. Lemkul [[email protected]] Sent: Tuesday, April 14, 2009 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the position_restraints He, Yang wrote: > HI all users, > > I want to define the position_restraints in the itp file but when I run it, > it always show that > > Segmentation fault (core dumped) > You'll have to do better than "run it" - what do you mean, grompp? mdrun? As written, your position restraints look OK, so I don't think the problem is related to that section, necessarily. How have you deduced that this is where the problem lies? Are you getting any other messages from (grompp? mdrun?) before the seg fault? -Justin > and I will list the part below: > > [position_restraints] > ;ai funct fc > 1 1 10000 10000 10000 > 2 1 10000 10000 10000 > 3 1 10000 10000 10000 > 4 1 10000 10000 10000 > 5 1 10000 10000 10000 > 6 1 10000 10000 10000 > 7 1 10000 10000 10000 > 8 1 10000 10000 10000 > 9 1 10000 10000 10000 > 10 1 10000 10000 10000 > 11 1 10000 10000 10000 > 12 1 10000 10000 10000 > 13 1 10000 10000 10000 > 14 1 10000 10000 10000 > 15 1 10000 10000 10000 > 16 1 10000 10000 10000 > 17 1 10000 10000 10000 > 18 1 10000 10000 10000 > 19 1 10000 10000 10000 > 20 1 10000 10000 10000 > 41 1 10000 10000 10000 > 42 1 10000 10000 10000 > 43 1 10000 10000 10000 > 44 1 10000 10000 10000 > 45 1 10000 10000 10000 > 46 1 10000 10000 10000 > 47 1 10000 10000 10000 > 48 1 10000 10000 10000 > 49 1 10000 10000 10000 > 50 1 10000 10000 10000 > 51 1 10000 10000 10000 > 52 1 10000 10000 10000 > 53 1 10000 10000 10000 > 54 1 10000 10000 10000 > 55 1 10000 10000 10000 > 56 1 10000 10000 10000 > 57 1 10000 10000 10000 > 58 1 10000 10000 10000 > 59 1 10000 10000 10000 > 60 1 10000 10000 10000 > > Can anyone of you tell me what is the problem for that? Thank you very much > in advance. > > Yang > _______________________________________________ > 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 > -- ======================================== Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ 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 _______________________________________________ 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
