Hello all, I have a naphthalene + water system which I want to run a NPT simulation of. The system has been energy mininimized. When I run the NPT simulation using gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same simulation using 4.5.4 it crashes with lincs error. We have tried various things like energy minimizing multiple times using 4.5.4 but it still crashes. I have also changed the thermostat and barostat to Berendsen, the problem persists.
Has anything changed between the two versions that could lead to this trouble? I am pasted the mdp file below and also the last few lines of the error message I get from Gromacs 4.5.4. Thanks for your help. Sapna ************ MDP FILE ********* title = NPH + water ; a string dt = 0.002 ; time step nsteps = 12500000 ; number of steps comm-grps = system comm-mode = Linear nstcomm = 10 ; reset c.o.m. motion nstxout = 000 ; write coords nstvout = 000 ; write velocities nstlog = 2500 ; print to logfile nstenergy = 500 ; print energies xtc_grps = System nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw = 1.00 ; cut-off for vdw rcoulomb = 1.00 ; cut-off for coulomb rlist = 1.00 ; cut-off for coulomb Tcoupl = Nose-Hoover ref_t = 280.0 tc-grps = System tau_t = 0.5 DispCorr = EnerPres ; long range correction gen_vel = yes ; generate init. vel gen_temp = 280 ; init. temp. gen_seed = 372340 ; random seed constraints = h-bonds ; constraining bonds with H constraint_algorithm = lincs refcoord-scaling = no Pcoupl = Parrinello-Rahman Pcoupltype = isotropic ; pressure geometry tau_p = 1.0 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; ref pressure nsttcouple = 1 nstpcouple = 1 ***************** END MDP File *************** *********** Error Message ************* Program mdrun_sp, VERSION 4.5.4 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (4811) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- *********** End Error Message ************* -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-4-5-4-and-Gromacs-4-5-5-give-different-results-tp5009424.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
