Hi Justin, I will list my mdp file below:
integrator = sd dt = 0.001 nsteps = 200000 comm_mode = Linear ; Linear, None, Angular nstcomm = 0 comm-grps = System nstfout = 0 nstxout = 1000 nstvout = 1000 nstlog = 1000nstenergy = 100 nstxtcout = 100 xtc_grps = System energygrps = DNA energygrp_excl = nstlist = 0 ns_type = simple pbc = no ; xyz, no (vacuum), full (infinite) rlist = 0 coulombtype = Cut-off rcoulomb = 0 vdwtype = Cut-off rvdw = 0 tcoupl = no ; for sd, tcoupl is ignored tc-grps = System tau_t = 0.0347 ref_t = 270 pcoupl = no gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = none ; none, all-bonds freezegrps = freezedim = Thank you for your further suggestion. Yang ________________________________________ From: [email protected] [[email protected]] On Behalf Of Justin A. Lemkul [[email protected]] Sent: Tuesday, April 14, 2009 3:29 PM To: Gromacs Users' List Subject: Re: [gmx-users] the position_restraints He, Yang wrote: > 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. > This is difficult to diagnose exactly. To me, removal of position restraints suggests that you are fixing in place some bad contact that is causing your system to crash. Have a look at the trajectory to see what is going on. Did EM work properly? If you are still having trouble, post a more complete description of your system, relevant .mdp file(s), and anything else necessary to try to get a resolution. -Justin > 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 > -- ======================================== 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? 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