Goodmorning,
I am trying to perform a very simple dynamic of an atom of Cu2+ in a box of tip3p water using the OPLS force field on GROMACS 5.0.4. I have done an energy minimization using the steepest algorythm and equilibrations in NVT and NPT ensemble, but during the mdrun of the dynamics I got a 'segmentation fault' and the system seems to blow up after 6 steps. This is the mdrun output: starting mdrun 'Copper in water' 2500000 steps, 5000.0 ps. step 0 step 2: Water molecule starting at atom 58 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 2: Water molecule starting at atom 58 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step2b.pdb to ./#step2b.pdb.1# Back Off! I just backed up step2c.pdb to ./#step2c.pdb.1# Wrote pdb files with previous and current coordinates step 3: Water molecule starting at atom 343 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 3: Water molecule starting at atom 343 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step3b.pdb to ./#step3b.pdb.1# Back Off! I just backed up step3c.pdb to ./#step3c.pdb.1# Wrote pdb files with previous and current coordinates step 4: Water molecule starting at atom 343 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 4: Water molecule starting at atom 343 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step4b.pdb to ./#step4b.pdb.1# Back Off! I just backed up step4c.pdb to ./#step4c.pdb.1# Wrote pdb files with previous and current coordinates step 5: Water molecule starting at atom 343 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 5: Water molecule starting at atom 343 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step5b.pdb to ./#step5b.pdb.1# Back Off! I just backed up step5c.pdb to ./#step5c.pdb.1# Wrote pdb files with previous and current coordinates step 6: Water molecule starting at atom 343 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 6: Water molecule starting at atom 343 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step6b.pdb to ./#step6b.pdb.1# Back Off! I just backed up step6c.pdb to ./#step6c.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault (core dump creato) THIS IS MY .MDP FILE FOR THE DYNAMICS: ; Run control integrator = sd ; Langevin dynamics dt = 0.002 nsteps = 2500000 ; 5 ns nstcomm = 100 ; Output control nstxout = 1000 nstvout = 1000 nstfout = 1000 nstlog = 1000 nstenergy = 1000 nstxout-compressed = 1000 ; Neighborsearching and short-range nonbonded interactions cutoff-scheme = verlet nstlist = 10 ns_type = grid pbc = xyz rlist = 0.8 ; Electrostatics coulombtype = PME rcoulomb = 1.2 ; van der Waals vdwtype = cutoff rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tcoupl = Nose-Hoover tc_grps = system tau_t = 1.0 ref_t = 298.15 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-05 ref_p = 1.0 refcoord_scaling = com ; centre of mass ; Free energy control stuff ; Generate velocities to start gen_vel = no gen_temp = 298.15 gen_seed = -1 ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 lincs-iter = 1 THIS IS MY TOPOLOGY FILE: ; Topology for Copper in SPCE #include "oplsaa.ff/forcefield.itp" ; water topology #include "oplsaa.ff/spce.itp" ;Cu topology [ moleculetype ] ; molname nrexcl CU 1 [ atoms ] ; id at type res nr residu name at name cg nr charge mass 1 Cu2+ 1 CU CU 1 2 63.54600 [ system ] ; Name Copper in water [ molecules ] ; Compound #mols SOL 1000 Cu 1 I've already read the material in the web for this 'segmentation fault', but every single case seems to be different. In addition, I'm wondering if it could be a bug or just a simple blowing up. Sorry if I wrote something unsophisticated, but I am a new gromacs user. Thank you in advance. Matteo Busato -- 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.