Dear GROMACS users, I'm doing this tutorial: https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf and I have an error with dt=0.002 or even dt=0.001 in pr.mdp during equilibration. It works only with dt=0.0001 which seems very very small step for me. Is it ok or I need to clean up the warnings like in error below(it's for dt=0.002):
starting mdrun 'T4-*LYPOZYME in water' 25000 steps, 50.0 ps. Warning: 1-4 interaction between 2 and 20 at distance 2.619 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 0.000 ps: Water molecule starting at atom 100062 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1# Wrote pdb files with previous and current coordinates step 0Segmentation fault and...@linux-f29d:~/GROMACS_MD/1LYD> Here is pr.mdp: integrator = md nsteps = 25000 dt = 0.001 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 Pcoupl = Berendsen tau-p = 1.0 compressibility = 5e-5 5e-5 5e-5 0 0 0 ref-p = 1.0 nstenergy = 100 define = -DPOSRES _______________________________________________ gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
