RE: [gmx-users] freeze group gives Segmentation fault
Hi, I don't understand your mail. Do you really get a segmentation fault, but also frames in your trajectory file? I think I fixed the freezing of the whole system bug. I tested it for a water system and it runs fine. Maybe you have constraints in your system. Asking your system to be completely frozen and to obey the constraints is usually contradictory. Therefore you system might still move slightly to try to obey the constraints. Anyhow it seems pretty useless to me to simulate a completely frozen system. Berk > From: [EMAIL PROTECTED] > Date: Mon, 10 Nov 2008 15:13:06 +0100 > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] freeze group gives Segmentation fault > > > I just tried Gromacs 4.0.2. It still gives a Segmentation fault: > > "Reading file topol.tpr, VERSION 4.0.2 (single precision) > Loaded with Money > > Segmentation fault" > > I did a test, putting the whole system into one freezegroup. Then the > simulation starts running. But some of the atoms belonging to the > "freeze-group" still move: The RMSD keeps growing and the Potential > Energy = -132 kJ/mol. Reading in the trajectory with vmd shows the > molecules moving. There is no pattern in the motion though. I checked > the index.ndx twice - there is no mistake in there. > > Ilona > > > > There was a bug in the freeze group code that got fixed today. I > > don't know anything else about it. Please update your source code > > and try again. > > > > Mark > > > > [EMAIL PROTECTED] wrote: > >> > >> Using freezegroups I get a Segmentation fault. The simulation does > >> not start, so the output is empty. > >> > >> "Reading file topol.tpr, VERSION 4.0_rc4 (single precision) > >> Segmentation fault" > > > > > _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] freeze group gives Segmentation fault
I just tried Gromacs 4.0.2. It still gives a Segmentation fault: "Reading file topol.tpr, VERSION 4.0.2 (single precision) Loaded with Money Segmentation fault" I did a test, putting the whole system into one freezegroup. Then the simulation starts running. But some of the atoms belonging to the "freeze-group" still move: The RMSD keeps growing and the Potential Energy = -132 kJ/mol. Reading in the trajectory with vmd shows the molecules moving. There is no pattern in the motion though. I checked the index.ndx twice - there is no mistake in there. Ilona There was a bug in the freeze group code that got fixed today. I don't know anything else about it. Please update your source code and try again. Mark [EMAIL PROTECTED] wrote: Using freezegroups I get a Segmentation fault. The simulation does not start, so the output is empty. "Reading file topol.tpr, VERSION 4.0_rc4 (single precision) Segmentation fault" ; ; File 'mdout.mdp' was generated ; By user: bq_ibaldus (2417) ; On host: cln-fg06 ; At date: Fri Nov 7 15:53:11 2008 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= none ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 0.01 emstep = 0.01 ; Max number of iterations in relax_shells niter= 100 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 1 nstfout = 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = crystal ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.5 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off rcoulomb_switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii
Re: [gmx-users] freeze group gives Segmentation fault
[EMAIL PROTECTED] wrote: Hi! I am trying to use freezegroups on an ice-crystal. grompp gives no warning. Trying the same simulation but removing the freezegroup works. We're not mind-readers :-) Why do you think it's not working? What do you see on stdout? In the various output files? Please note my mdp-file's attached That's a start. It's a bit like taking one's car to the mechanic. The fact that you brought it in means you think something's probably wrong, but it'll cost you a lot more or take lots more time if you don't tell them things you've found out. Mark ___ gmx-users mailing listgmx-users@gromacs.org 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] freeze group gives Segmentation fault
Hi! I am trying to use freezegroups on an ice-crystal. grompp gives no warning. Trying the same simulation but removing the freezegroup works. Please note my mdp-file's attached Ilona ; ; File 'mdout.mdp' was generated ; By user: bq_ibaldus (2417) ; On host: cln-fg06 ; At date: Fri Nov 7 15:53:11 2008 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= none ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 0.01 emstep = 0.01 ; Max number of iterations in relax_shells niter= 100 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 1 nstfout = 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = crystal ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.5 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off rcoulomb_switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = Berendsen ; Groups to couple separately tc_grps = crystal ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t
