Hi Justin, I have used the same files to re-run using gromacs-4.5.4 and the only difference is that I get a "segmentation fault" instead of "bus error" message. Thanks for your help, I will then fill out the issue report as you suggested.
Best, Thereza Professor Thereza A. Soares Departamento de Química Fundamental Universidade Federal de Pernambuco Av. Jornalista Anibal Fernandes, s/nº Cidade Universitária 50740-560 Recife, PE, Brazil tel: +558121268440 fax: +558121268442 thereza.soa...@ufpe.br website@dqf http://dqfnet.ufpe.br/biomat/ On Jun 27, 2011, at 12:06 PM, gmx-users-requ...@gromacs.org wrote: > > Date: Mon, 27 Jun 2011 10:28:46 -0300 > From: Thereza Soares <thereza.soa...@ufpe.br> > Subject: [gmx-users] Comparing MD ensembles with exp. NOE restraints > --> bus error > To: gmx-users@gromacs.org > Message-ID: <032ec9e3-5b6e-466c-a785-3adfc44f4...@ufpe.br> > Content-Type: text/plain; charset=windows-1252 > > Hi There, > > I would like to compare my ensemble of (unrestrained) MD structures against > experimental NOE distances. For that, I have added the distance_restraints > block to my *.top file such as: > > [distance_restraints] > ;ai aj type index type‚ low up1 up2 fac > 33 31 1 0 1 0.0 3.000 1.2 0.4 > 35 31 1 1 1 0.0 2.500 0.7 0.3 > > I have also added the disre options below to the *.mdp file used to generate > a new tpr for the NOE analysis > > disre = Simple > disre-weighting = Equal > disre-mixed = no > disre-fc = 1000 > disre-tau = 0 > nstdisreout = 1 > > When I run g_disre -s proton.tpr -f trj.pdb, it reads the tpr file and gives > a bus error ... I am copying the entire mdp file in case someone can point me > out what is wrong with it. > > > I would appreciate any suggestions on what maybe wrong here, > > Cheers, > > Thereza > > integrator = md > dt = 0.002 > nsteps = 25000000 > nstxout = 500 > nstvout = 500 > nstlog = 500 > nstenergy = 500 > nstxtcout = 500 > comm-mode = Linear > nstcomm = 5 > comm-grps = SYSTEM > xtc_grps = SYSTEM > energygrps = SYSTEM > nstlist = 5 > rlist = 1.4 > coulombtype = generalized-reaction-field > epsilon_rf = 66.0 > ns_type = grid > rcoulomb = 1.4 > rvdw = 1.4 > pbc = xyz > tcoupl = berendsen > tc-grps = SYSTEM > tau_t = 0.2 > ref_t = 300 > Pcoupl = berendsen > Pcoupltype = semi-isotropic > tau_p = 0.4 0.4 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > gen_vel = yes > gen_temp = 10 > gen_seed = 178296 > constraints = h-bonds > disre = simple > disre-weighting = equal > disre-mixed = no > disre-fc = 1000 > disre-tau = 0 > nstdisreout = 1 > > > > > > ------------------------------ > > Message: 2 > Date: Mon, 27 Jun 2011 09:49:29 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Comparing MD ensembles with exp. NOE > restraints --> bus error > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e088a69.7080...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > Thereza Soares wrote: >> Hi There, >> >> I would like to compare my ensemble of (unrestrained) MD structures against >> experimental NOE distances. For that, I have added the distance_restraints >> block to my *.top file such as: >> >> [distance_restraints] >> ;ai aj type index type‚ low up1 up2 fac >> 33 31 1 0 1 0.0 3.000 1.2 0.4 >> 35 31 1 1 1 0.0 2.500 0.7 0.3 >> >> >> I have also added the disre options below to the *.mdp file used to generate >> a new tpr for the NOE analysis >> >> disre = Simple >> disre-weighting = Equal >> disre-mixed = no >> disre-fc = 1000 >> disre-tau = 0 >> nstdisreout = 1 >> >> When I run g_disre -s proton.tpr -f trj.pdb, it reads the tpr file and gives >> a bus error ... I am copying the entire mdp file in case someone can point me >> out what is wrong with it. >> > > There is nothing wrong with the .mdp file. There is likely a bug in the > g_disre > code somewhere, as is usually the case with immediate bus errors or > segmentation > faults. > >> >> I would appreciate any suggestions on what maybe wrong here, >> > > You haven't mentioned which version of Gromacs you're using, but if it is not > 4.5.4 (the latest), please try again with this version. If you are using > 4.5.4 > or the error persists, please file an issue report on redmine.gromacs.org and > include your .tpr and .pdb files necessary to reproduce the problem. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
