Dear GMX user, I have just installed *gromacs 2016.1* on my machine and run mdrun with these option: ------------------------------------------------------------------------------------------------- title = 50AT DNA MD simulation ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000 ; 2 * 5000000 = 10000 ps (10 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 20.0 ps nstvout = 500 ; save velocities every 20.0 ps nstenergy = 500 ; save energies every 20.0 ps nstlog = 500 ; update log file every 20.0 ps nstxout-compressed = 500 ; save compressed coordinates every 20.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = SYSTEM ; replaces xtc-grps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 40 ; 20 fs, largerly irrelevant with Verlet scheme rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order =5 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat nsttcouple = 1 tc-grps = DNA SOL ION ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 298 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ;do not generate Velocity ------------------------------------------------------------------------------------------------- *After that, I use trjconv to get position of DNA by command:* gmx trjconv -s md.tpr -f md.xtc -o md_mol.xtc -pbc mol -ur compact and gmx prompt: Group 0 ( System) has 500179 elements Group 1 ( DNA) has 3198 elements Group 2 ( NA) has 129 elements Group 3 ( CL) has 31 elements Group 4 ( Water) has 496821 elements Group 5 ( SOL) has 496821 elements Group 6 ( non-Water) has 3358 elements Group 7 ( Ion) has 160 elements Group 8 ( NA) has 129 elements Group 9 ( CL) has 31 elements Group 10 ( Water_and_ions) has 496981 elements
*I type 1 and press Enter then get message:* Select a group: 1 Selected 1: 'DNA' Reading frame 0 time 0.000 Precision of md.xtc is 0.001 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up md_mol.xtc to ./#md_mol.xtc.2# *** Error in `gmx': malloc(): memory corruption: 0x0000000001be5c30 *** Aborted *Could you tell me this error is caused by me or gromacs program?* *Thank you* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.